Genes and proteins associated with angiogenesis and uses thereof

ABSTRACT

Disclosed is a panel of biomarkers associated with angiogenesis, and the use of such biomarkers (genes, proteins, homologues and analogs thereof) to regulate angiogenesis. Methods for identifying compounds useful for regulating angiogenesis and conditions related thereto are disclosed.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of priority under 35 U.S.C. § 119(e) from U.S. Provisional Application No. 60/722,694, filed Sep. 30, 2005 and from U.S. Provisional Application No. 60/816,969, filed Jun. 27, 2006. The entire disclosure of each of U.S. Provisional Application No. 60/722,694 and U.S. Provisional Application No. 60/816,969 is incorporated herein by reference in its entirety.

GOVERNMENT SUPPORT

This invention was made in part with government support under NIH Grant No. CA095519 and NIH Grant No. CA99321, each awarded by the National Institutes of Health. The government has certain rights to this invention.

REFERENCE TO SEQUENCE LISTING

This application contains a Sequence Listing submitted on a compact disc, in duplicate. Each of the two compact discs, which are identical to each other pursuant to 37 CFR § 1.52(e)(4), contains the following file: “Sequence Listing”, having a size in bytes of 266 KB, recorded on 2 Oct. 2006. The information contained on the compact disc is hereby incorporated by reference in its entirety pursuant to 37 CFR § 1.77(b)(4).

FIELD OF THE INVENTION

The present invention generally relates to genes and proteins, including homologues and agonist or antagonist analogs thereof, as targets for regulating angiogenesis. The present invention also relates to methods to identify regulators of angiogenesis using such biomarkers, and methods related thereto.

BACKGROUND OF THE INVENTION

Angiogenesis is the process whereby new blood vessels are formed from preexisting vessels; it is a highly regulated event that encompasses a coordinated cascade of gene expression and repression, and one that is influenced by many factors, including a variety of environmental cues provided by the extracellular matrix (ECM) (Sottile, 2004; Stupack and Cheresh, 2002). Cancer cells play a vital role in eliciting many of these environmental cues in part via their ability to produce and secrete numerous angiogenic factors and proteases that create tumor microenvironments conductive to angiogenesis (Bissell et al, 2002; Pupa et al, 2002; Sottile, 2004). Although previously believed to be innocent bystanders during angiogenic reactions, it is becoming increasingly apparent that endothelial cells (ECs) also make important contributions to the activation and resolution of angiogenesis. Indeed, ECs generate a variety of environmental cues that shape and remodel tumor and vascular microenvironments, ultimately leading to altered vessel development (Davis and Senger, 2005; Sottile, 2004). Unfortunately, the molecular mechanisms whereby ECs and the molecules they secrete actively direct angiogenesis activation and resolution remain to be determined definitively. It is known that tumor angiogenesis depends upon the coordinated cooperation between cancer and endothelial cells (ECs), and results in the formation and infiltration of new vessels into tumor microenvironments, thereby providing developing tumors with a source of nutrients and oxygen, as well as a route for cancer cell metastasis (Carmeliet and Jain, 2000; Folkman and Shing, 1992). Failure to establish these cancer:EC connections prevents the development and progression of small, innocuous cancer growths, and as such, tumors remain in a dormant, benign state (Bergers and Benjamin, 2003; Hanahan and Folkman, 1996). Recently, significant inroads in understanding of the role of cancer cells in mediating tumor angiogenesis and EC activation have taken place. Indeed, cancer cells actively induce tumor angiogenesis via their ability to produce and secrete a variety of pro-angiogenic factors (Liotta and Kohn, 2001; Stupack and Cheresh, 2002), a process known as the angiogenic switch (Bergers and Benjamin, 2003; Hanahan and Folkman, 1996). In contrast, comparably little is known concerning the role of ECs during this process, particularly the functional consequences of their ability to remodel vascular and tumor microenvironments during angiogenesis. Although ECs are known to remodel their microenvironment by secreting various extracellular proteases, such as MMPs (matrix metalloproteases), ADAMs (a disintegrin and metalloprotease domain), and ADAMTS (a disintegrin and metalloprotease domain with thrombospondin motifs; Stupack and Cheresh, 2002), a thorough understanding of how these molecules and their stromal targets mediate angiogenesis activation or resolution remains incompletely understood. Thus, identifying and characterizing novel proteins secreted by angiogenic ECs will offer important insights into the role of the endothelium in mediating angiogenesis, as well as its potential to be targeted therapeutically to prevent tumor angiogenesis. Specifically, mapping and defining the EC secretome will significantly enhance understanding of angiogenesis, as well as identify novel therapeutic agents and/or targets that can be exploited to prevent tumor angiogenesis and metastasis in cancer patients.

SUMMARY OF THE INVENTION

One embodiment of the present invention relates to a method to regulate angiogenesis in cells or a tissue of a patient. The method comprises regulating the expression or biological activity in the cells or tissue of any one or more biomarkers selected from a biomarker represented in any one or more of Table I, Table IV, Table V, and/or Table VI.

In one aspect of this embodiment, the biomarkers are any one or more of the biomarkers in Table VI. In another aspect of this embodiment, the biomarkers are any one or more of the biomarkers selected from: ADAMts7, CRELD-2, Decorin, ECM1, Inhibin β-b, Integrin α-3, Integrin α-6, Lipocalin-7, Loxl-3, Lumican, MAGP-2, Matrilin-2, Nephronectin, SerpinE2, and/or SMOC-2.

In another aspect of this embodiment, the biomarkers are any one or more of the biomarkers selected from: 0610007C21Rik, apoptosis related protein APR-3, 1810014L12Rik, Cd14 (encoding CD14 antigen represented herein by SEQ ID NO:5 and SEQ ID NO:6), Cd38 (comprising a nucleic acid sequence represented herein by SEQ ID NO:7 and encoding CD38 antigen); Cd53 (encoding CD53 antigen represented herein by SEQ ID NO:8 and SEQ ID NO:9), Emp2 (encoding epithelial membrane protein represented herein by SEQ ID NO:10 and SEQ ID NO:11), Fcgrt (encoding Fc receptor (IgG, alpha chain transporter) represented herein by SEQ ID NO:12 and SEQ ID NO:13), Islr (encoding immunoglobulin superfamily containing leucine-rich repeat represented herein by SEQ ID NO:14 and SEQ ID NO:15); Lrp2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:16 and SEQ ID NO:17 and encoding low density lipoprotein receptor-related protein 2); Ly6a (encoding lymphocyte antigen 6 complex, locus A represented herein by SEQ ID NO:18); P2rx4 (encoding purinergic receptor P2X, ligand-gated ion channel 4, represented herein by SEQ ID NO:19 and SEQ ID NO:20; Pcdhb9 (encoding protocadherin beta 9 represented herein by SEQ ID NO:21 and SEQ ID NO:22); Ptpre (encoding protein tyrosine phosphatase receptor type E represented herein by SEQ ID NO:23 and SEQ ID NO:24); Slc4a3 (encoding solute carrier family 4 (anion exchanger) member 3, represented herein by SEQ ID NO:25 and SEQ ID NO:26); and/or Tmc6 (encoding transmembrane channel-like gene family 6, represented herein by SEQ ID NO:27).

In another aspect of this embodiment, the biomarkers are any one or more of the biomarkers selected from: 9130213B05Rik (encoding a protein represented herein by SEQ ID NO:29); C1s (encoding complement component 1, s subcomponent, represented herein by SEQ ID NO:34 and SEQ ID NO:35); C3 (encoding complement component 3 represented herein by SEQ ID NO:30 and SEQ ID NO:31); Cfh (comprising a nucleic acid sequence represented herein by SEQ ID NO:32 and SEQ ID NO:33 and encoding complement component factor h); Col9a3 (comprising a nucleic acid sequence represented herein by SEQ ID NO:36 and SEQ ID NO:37 and encoding procollagen, type IX, alpha 3); Grem1 (encoding cysteine knot superfamily 1, BMP antagonist 1, represented herein by SEQ ID NO:38 and SEQ ID NO:39); Loxl3 (encoding lysyl oxidase-like 3, represented herein by SEQ ID NO:40 and SEQ ID NO:41); MAGP-2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:124 and SEQ ID NO:125 and encoding microfibrillar associated protein 5, represented herein by SEQ ID NO:42 and SEQ ID NO:43); Mglap (encoding matrix gamma-carboxyglutamate (gla) protein represented herein by SEQ ID NO:44 and SEQ ID NO:45); Naga (encoding N-acetyl galactosaminidase, alpha, represented herein by SEQ ID NO:46 and SEQ ID NO:47); Nbl1 (encoding neuroblastoma, suppression of tumorigenicity 1, represented herein by SEQ ID NO:48 and SEQ ID NO:49); Ngfb (encoding nerve growth factor, beta, represented herein by SEQ ID NO:50 and SEQ ID NO:51), Npnt (represented herein by SEQ ID NO:52 and SEQ ID NO:53 and encoding nephronectin); Olfm1 (encoding olfactomedin 1, represented herein by SEQ ID NO:54 and SEQ ID NO:55); and/or U90926 (encoding a protein represented herein by SEQ ID NO:56).

Any combinations of any of the above-identified biomarkers are included in the invention. In a preferred aspect of this embodiment, the biomarker is MAGP-2.

In one aspect, the step of regulating comprises contacting the cells or tissue of from the patient with an antagonist of the biomarker. In another aspect, the step of regulating comprises contacting the cells or tissue of from the patient with the biomarker or a biologically active homologue or agonist thereof. In another aspect, the step of regulating comprises expressing a recombinant nucleic acid molecule encoding the biomarker or a homologue thereof in the tissue of the patient.

In one aspect of this embodiment, angiogenesis is upregulated. Such an aspect of the invention can be used to treat a patient that has vascular deficiencies, cardiovascular disease, or would benefit from stimulation of endothelial cell activation and stabilization of newly formed microvessels or other vessels, such as in ischemia or stroke.

In another aspect of this embodiment angiogenesis is downregulated. Such an aspect of the invention can be used to treat conditions that are characterized or caused by abnormal or excessive angiogenesis, including, but are not limited to: cancer (e.g., activation of oncogenes, loss of tumor suppressors); infectious diseases (e.g., pathogens express angiogenic genes, enhance angiogenic programs); autoimmune disorders (e.g., activation of mast cells and other leukocytes); vascular malformations (e.g., Tie-2 mutation); DiGeorge syndrome (e.g., low VEGF and neuropilin-1 expression); HHT (e.g., mutations of endoglin or LK-1), cavernous hemangioma (e.g., loss of Cx37 and Cx40); atherosclerosis; transplant ateriopathy; obesity (e.g., angiogenesis induced by fatty diet, weight loss by angiogenesis inhibitors); psoriasis; warts; allergic dermatitis; scar keloids; pyogenic granulomas; blistering disease; Kaposi sarcoma in AIDS patients; persistent hyperplastic vitreous syndrome (e.g., loss of Ang-2 or VEGF164); diabetic retinopathy; retinopathy of prematurity; choroidal neovascularization (e.g., TIMP-3 mutation); primary pulmonary hypertension (e.g., germline BMPR-2 mutation, somatic EC mutation); asthma; nasal polyps; inflammatory bowel disease; periodontal disease; ascites; peritoneal adhesions; endometriosis; uterine bleeding; ovarian cysts; ovarian hyperstimulation; arthritis; synovitis; osteomyelitis; and/or osteophyte formation.

Another embodiment of the present invention relates to a method to reduce tumorigenicity in a patient, comprising regulating the expression or biological activity of any one or more biomarkers selected from a biomarker represented in any one or more of Table I, Table IV, Table V, and/or Table VI. In one aspect of this embodiment, the biomarkers are any one or more of the biomarkers in Table VI.

In another aspect of this embodiment, the biomarkers are any one or more of the biomarkers selected from: ADAMts7, CRELD-2, Decorin, ECM1, Inhibin β-b, Integrin α-3, Integrin α-6, Lipocalin-7, Loxl-3, Lumican, MAGP-2, Matrilin-2, Nephronectin, SerpinE2, and/or SMOC-2.

In another aspect of this embodiment, the biomarkers are any one or more of the biomarkers selected from: 0610007C21Rik, apoptosis related protein APR-3, 1810014L12Rik, Cd14 (encoding CD14 antigen represented herein by SEQ ID NO:5 and SEQ ID NO:6), Cd38 (comprising a nucleic acid sequence represented herein by SEQ ID NO:7 and encoding CD38 antigen); Cd53 (encoding CD53 antigen represented herein by SEQ ID NO:8 and SEQ ID NO:9), Emp2 (encoding epithelial membrane protein represented herein by SEQ ID NO:10 and SEQ ID NO:11), Fcgrt (encoding Fc receptor (IgG, alpha chain transporter) represented herein by SEQ ID NO:12 and SEQ ID NO:13), Islr (encoding immunoglobulin superfamily containing leucine-rich repeat represented herein by SEQ ID NO:14 and SEQ ID NO:15); Lrp2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:16 and SEQ ID NO:17 and encoding low density lipoprotein receptor-related protein 2); Ly6a (encoding lymphocyte antigen 6 complex, locus A represented herein by SEQ ID NO:18); P2rx4 (encoding purinergic receptor P2X, ligand-gated ion channel 4, represented herein by SEQ ID NO:19 and SEQ ID NO:20; Pcdhb9 (encoding protocadherin beta 9 represented herein by SEQ ID NO:21 and SEQ ID NO:22); Ptpre (encoding protein tyrosine phosphatase receptor type E represented herein by SEQ ID NO:23 and SEQ ID NO:24); Slc4a3 (encoding solute carrier family 4 (anion exchanger) member 3, represented herein by SEQ ID NO:25 and SEQ ID NO:26); and/or Tmc6 (encoding transmembrane channel-like gene family 6, represented herein by SEQ ID NO:27).

In yet another aspect of this embodiment, the biomarkers are any one or more of the biomarkers selected from: 9130213B05Rik (encoding a protein represented herein by SEQ ID NO:29); C1s (encoding complement component 1, s subcomponent, represented herein by SEQ ID NO:34 and SEQ ID NO:35); C3 (encoding complement component 3 represented herein by SEQ ID NO:30 and SEQ ID NO:31); Cfh (comprising a nucleic acid sequence represented herein by SEQ ID NO:32 and SEQ ID NO:33 and encoding complement component factor h); Col9a3 (comprising a nucleic acid sequence represented herein by SEQ ID NO:36 and SEQ ID NO:37 and encoding procollagen, type IX, alpha 3); Grem1 (encoding cysteine knot superfamily 1, BMP antagonist 1, represented herein by SEQ ID NO:38 and SEQ ID NO:39); Loxl3 (encoding lysyl oxidase-like 3, represented herein by SEQ ID NO:40 and SEQ ID NO:41); MAGP-2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:124 and SEQ ID NO:125 and encoding microfibrillar associated protein 5, represented herein by SEQ ID NO:42 and SEQ ID NO:43); Mglap (encoding matrix gamma-carboxyglutamate (gla) protein represented herein by SEQ ID NO:44 and SEQ ID NO:45); Naga (encoding N-acetyl galactosaminidase, alpha, represented herein by SEQ ID NO:46 and SEQ ID NO:47); Nbl1 (encoding neuroblastoma, suppression of tumorigenicity 1, represented herein by SEQ ID NO:48 and SEQ ID NO:49); Ngfb (encoding nerve growth factor, beta, represented herein by SEQ ID NO:50 and SEQ ID NO:51), Npnt (represented herein by SEQ ID NO:52 and SEQ ID NO:53 and encoding nephronectin); Olfm1 (encoding olfactomedin 1, represented herein by SEQ ID NO:54 and SEQ ID NO:55); and/or U90926 (encoding a protein represented herein by SEQ ID NO:56).

Any combinations of any of the above-identified biomarkers are included in the invention. In a preferred aspect of this embodiment, the biomarker is MAGP-2.

Another embodiment of the present invention relates to a method to identify a compound that regulates angiogenesis. The method includes the steps of: (a) detecting an initial level of the expression or activity of one or more biomarkers in a cell or soluble product derived therefrom, wherein the biomarker is a biomarker selected from a biomarker represented in any one or more of Table I, Table IV, Table V, and Table VI; (b) contacting the cell with a test compound; (c) detecting a level of the biomarker expression or activity in the cell or soluble product derived therefrom after contact of the cell with the compound; and, (d) selecting a compound that changes the level of biomarker expression or activity in the cell or soluble product therefrom, as compared to in the absence of the compound and/or as compared to the initial level of biomarker expression or activity, as a compound that regulates angiogenesis.

In one aspect of this embodiment, the biomarkers are any one or more of the biomarkers in Table VI.

In another aspect of this embodiment, the biomarkers are any one or more of the biomarkers selected from: ADAMts7, CRELD-2, Decorin, ECM1, Inhibin β-b, Integrin α-3, Integrin α-6, Lipocalin-7, Loxl-3, Lumican, MAGP-2, Matrilin-2, Nephronectin, SerpinE2, and/or SMOC-2.

In another aspect of this embodiment, the biomarkers are any one or more of the biomarkers selected from: 0610007C21Rik, apoptosis related protein APR-3, 1810014L12Rik, Cd14 (encoding CD14 antigen represented herein by SEQ ID NO:5 and SEQ ID NO:6), Cd38 (comprising a nucleic acid sequence represented herein by SEQ ID NO:7 and encoding CD38 antigen); Cd53 (encoding CD53 antigen represented herein by SEQ ID NO:8 and SEQ ID NO:9), Emp2 (encoding epithelial membrane protein represented herein by SEQ ID NO:10 and SEQ ID NO:11), Fcgrt (encoding Fc receptor (IgG, alpha chain transporter) represented herein by SEQ ID NO:12 and SEQ ID NO:13), Islr (encoding immunoglobulin superfamily containing leucine-rich repeat represented herein by SEQ ID NO:14 and SEQ ID NO:15); Lrp2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:16 and SEQ ID NO:17 and encoding low density lipoprotein receptor-related protein 2); Ly6a (encoding lymphocyte antigen 6 complex, locus A represented herein by SEQ ID NO:18); P2rx4 (encoding purinergic receptor P2X, ligand-gated ion channel 4, represented herein by SEQ ID NO:19 and SEQ ID NO:20; Pcdhb9 (encoding protocadherin beta 9 represented herein by SEQ ID NO:21 and SEQ ID NO:22); Ptpre (encoding protein tyrosine phosphatase receptor type E represented herein by SEQ ID NO:23 and SEQ ID NO:24); Slc4a3 (encoding solute carrier family 4 (anion exchanger) member 3, represented herein by SEQ ID NO:25 and SEQ ID NO:26); and/or Tmc6 (encoding transmembrane channel-like gene family 6, represented herein by SEQ ID NO:27).

In yet another aspect of this embodiment, the biomarkers are any one or more of the biomarkers selected from: 9130213B05Rik (encoding a protein represented herein by SEQ ID NO:29); C1s (encoding complement component 1, s subcomponent, represented herein by SEQ ID NO:34 and SEQ ID NO:35); C3 (encoding complement component 3 represented herein by SEQ ID NO:30 and SEQ ID NO:31); Cfh (comprising a nucleic acid sequence represented herein by SEQ ID NO:32 and SEQ ID NO:33 and encoding complement component factor h); Col9a3 (comprising a nucleic acid sequence represented herein by SEQ ID NO:36 and SEQ ID NO:37 and encoding procollagen, type IX, alpha 3); Grem1 (encoding cysteine knot superfamily 1, BMP antagonist 1, represented herein by SEQ ID NO:38 and SEQ ID NO:39); Loxl3 (encoding lysyl oxidase-like 3, represented herein by SEQ ID NO:40 and SEQ ID NO:41); MAGP-2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:124 and SEQ ID NO:125 and encoding microfibrillar associated protein 5, represented herein by SEQ ID NO:42 and SEQ ID NO:43); Mglap (encoding matrix gamma-carboxyglutamate (gla) protein represented herein by SEQ ID NO:44 and SEQ ID NO:45); Naga (encoding N-acetyl galactosaminidase, alpha, represented herein by SEQ ID NO:46 and SEQ ID NO:47); Nbl1 (encoding neuroblastoma, suppression of tumorigenicity 1, represented herein by SEQ ID NO:48 and SEQ ID NO:49); Ngfb (encoding nerve growth factor, beta, represented herein by SEQ ID NO:50 and SEQ ID NO:51), Npnt (represented herein by SEQ ID NO:52 and SEQ ID NO:53 and encoding nephronectin); Olfm1 (encoding olfactomedin 1, represented herein by SEQ ID NO:54 and SEQ ID NO:55); and/or U90926 (encoding a protein represented herein by SEQ ID NO:56).

Any combinations of any of the above-identified biomarkers are included in the invention. In a preferred aspect of this embodiment, the biomarker is MAGP-2.

Another embodiment of the invention relates to a method to identify a compound useful for inhibition of tumor growth or malignancy. The method includes the steps of: (a) detecting an initial level of the expression or activity of one or more biomarkers in a cell or soluble product derived therefrom, wherein the biomarker is a biomarker represented in any one or more of Table I, Table IV, Table V, and Table VI; (b) contacting the tumor cell with a test compound; (c) detecting a level of biomarker expression or activity in the tumor cell or soluble product derived therefrom after contact of the tumor cell with the compound; and, (d) selecting a compound that changes the level of the biomarker expression or activity in the tumor cell or soluble product therefrom, as compared to the initial level of biomarker expression or activity, toward a baseline level of biomarker expression or activity established from a non-tumor cell, wherein the selected compound is predicted to be useful for inhibition of tumor growth or malignancy.

Yet another embodiment of the present invention relates to a method for assessing the presence of tumor cells or potential therefore in a patient. The method includes the steps of: (a) detecting a level of expression or activity of the expression or activity of one or more biomarkers in a test sample from a patient to be diagnosed, wherein the biomarker is a biomarker represented in any one or more of Table I, Table IV, Table V, and Table VI; and (b) comparing the level of expression or activity of the biomarker in the test sample to a baseline level of biomarker expression or activity established from a control sample. Detection of a statistically significant difference in the biomarker expression or activity in the test sample, as compared to the baseline level of biomarker expression or biological activity, is an indicator of the presence of tumor cells or the potential therefore in the test sample as compared to cells in the control sample.

In one aspect of this embodiment, the step of detecting comprises detecting biomarker mRNA transcription by cells in the test sample. For example, such a step of detecting can be performed by a method selected from, but not limited to, polymerase chain reaction (PCR), reverse transcriptase-PCR (RT-PCR), in situ hybridization, Northern blot, sequence analysis, gene microarray analysis, and detection of a reporter gene. In one aspect, the step of detecting comprises detecting biomarker protein in the test sample. For example, such a step of detecting can be performed by a method selected from, but not limited to, immunoblot, enzyme-linked immunosorbant assay (ELISA), radioimmunoassay (RIA), immunoprecipitation, immunohistochemistry and immunofluorescence. In one aspect, the step of detecting comprises detecting biomarker biological activity in the test sample. For example, such a step of detecting can be performed by a method selected from, but not limited to, measuring proliferation of cells expressing the biomarker, measuring angiogenic sprouting of cells expressing the biomarker, and measuring migration and invasion ability of endothelial cells expressing the biomarker.

In one aspect of this embodiment, the test sample is from a source selected from the group consisting of: breast, kidney, ovary, colon, and uterus, in the patient. In another aspect, the test sample is from a patient being diagnosed for cancer and wherein the baseline level is established from a negative control sample that is established as non-tumorigenic.

In one aspect of this embodiment, the baseline level is established by a method selected from the group consisting of: (1) establishing a baseline level of biomarker expression or activity in an autologous control sample from the patient, wherein the autologous sample is from a same cell type, tissue type or bodily fluid type as the test sample of step (a); (2) establishing a baseline level of biomarker expression or activity from at least one previous detection of biomarker expression or activity in a previous test sample from the patient, wherein the previous test sample was of a same cell type, tissue type or bodily fluid type as the test sample of step (a); and, (3) establishing a baseline level of biomarker expression or activity from an average of control samples of a same cell type, tissue type or bodily fluid type as the test sample of step (a), the control samples having been obtained from a population of matched individuals.

Yet another embodiment of the invention relates to an assay kit for assessing angiogenesis or the presence of tumor cells in a patient, comprising: (a) a reagent for detecting the expression or activity of a biomarker in a test sample, wherein the biomarker is a biomarker represented in any one or more of Table I, Table IV, Table V, and Table VI; and (b) a reagent for detecting a control marker characteristic of a cell or tissue type that is in the test sample or that is secreted into the test sample by the cell or tissue. In one aspect, the reagent of (a) is selected from the group consisting of: a hybridization probe of at least about 8 nucleotides that hybridizes under stringent hybridization conditions to a nucleic acid molecule encoding the biomarker or a fragment thereof; an oligonucleotide primer for amplification of mRNA encoding the biomarker or a fragment thereof; and an antibody that selectively binds to the biomarker. In one aspect, the reagent of (b) is selected from the group consisting of: a hybridization probe of at least about 8 nucleotides that hybridizes under stringent hybridization conditions to a nucleic acid molecule encoding the control marker or a fragment thereof; an oligonucleotide primer for amplification of mRNA encoding the control marker or a fragment thereof; and an antibody that selectively binds to the control marker. In one aspect, the reagents of (a) and (b) are suitable for use in a method of detection selected from the group consisting of immunohistochemistry and immunofluorescence.

Yet another embodiment of the invention relates to a method to reduce angiogenesis in cells or a tissue of a patient, comprising decreasing the expression or biological activity of Microfibril-associated glycoprotein-2 (MAGP-2) in the cells or tissue.

Another embodiment of the invention relates to a method to promote angiogenesis in cells or a tissue of a patient, comprising increasing the expression or biological activity of MAGP-2 in the cells or tissue.

Another embodiment of the invention relates to the use of MAGP-2 or a fragment or homologue thereof, or a nucleic acid molecule encoding MAGP-2 or a fragment or homologue thereof, or an agonist or antagonist of MAGP-2, in the preparation of a medicament for the regulation of angiogenesis.

BRIEF DESCRIPTION OF THE FIGURES OF THE INVENTION

FIG. 1A is a bar graph shows DNA synthesis (determined by measuring [³H]thymidine incorporation into cellular DNA) in serum-starved MB114 cells stably expressing either GFP or various putative angiogenic agents, stimulated in the absence or presence of either bFGF (50 ng/ml) or EGF (10 ng/ml) for 24 h at 37° C. (data are the mean (±SEM) of five independent experiments for MAGP-2 and SMOC-2, and of three independent experiments of CRELD-2; *, p<0.05; Student's T-Test).

FIG. 1B is a bar graph showing the invasion of MB114 cells expressing either GFP or various putative angiogenic agents through synthetic basement membranes over 48 h using a modified Boyden-chamber assay (data are the mean (±SEM) of three independent experiments; *, p<0.05; Student's T-Test).

FIGS. 1C and 1D are bar graphs showing p38 MAPK phosphorylation in serum-starved MB114 cells expressing MAGP-2 (FIG. 1C) or lumican (FIG. 1D), stimulated with either bFGF (50 ng/ml) or EGF (10 ng/ml) 0-15 min (data are the mean (±SEM) of 5 independent experiments; *, p<0.05; Student's T-Test).

FIG. 1E is a bar graph showing endothelial cell sprouting in MB114 cells expressing either GFP or various putative angiogenic agents (data are the mean (×SEM) of 5 independent experiments for lumican, SMOC-2, CRELD-2, MAGP-2, and Matrilin-2, and of three independent experiments for AK76 and ECM-1; *, p<0.05; Student's T-Test).

FIG. 2A shows that MAGP-2 (MAGP-2 purity was monitored by coomassie staining, and by immunoblotting with anti-FLAG M2 monoclonal antibodies (right panel)) promotes angiogenesis in vivo, as measured by angiogenic sprouting of quiescent MB114 cell monolayers (left panel) (data are the mean (±SEM) of two independent experiments; *, p<0.05; Student's T-Test).

FIG. 2B shows the results of subcutaneous injection of C57BL/6 female mice with Matrigel supplemented either with diluent (D), bFGF (50 ng/ml, LD; or 300 ng/ml, HD), or bFGF (50 ng/ml) in combination with MAGP-2 (1 μg/ml), where plugs were harvested and photographed (left panels), and then fixed, sectioned, and stained with Masson's trichrome to visualize infiltrating blood vessels (right panels; arrows denote blood vessels) (data are the mean (±SEM) of four independent experiments; *, **, ***, p<0.05; Student's Test).

FIG. 3A is a bar graph showing that MAGP-2 inhibits Hes-1 promoter activity in ECs (data are mean (±SEM) of 2 independent experiments).

FIG. 3B is a bar graph also showing that MAGP-2 inhibits Hes-1 promoter activity in ECs (data are the mean (±SEM) of four independent experiments; *, **, ***, p<0.05; Student's Test).

FIG. 4A shows Notch1 cleavage products (upper) and the densitometric analysis of Notch1 NICD production in response to experimental treatments (lower) in human 293T cells transiently transfected with cDNAs encoding Myc-tagged versions of Notch1, Jagged-1, and MAGP-2 in all combinations as indicated (data are the mean (±SEM) of four independent experiments; *, **, p<0.05; Student's T-Test; N, Notch1; N/M, Notch1 plus MAGP-2; N/J, Notch1 plus Jagged-1; N/J/M, Notch1, Jagged-1, and MAGP-2).

FIG. 4B shows luciferase activity after stimulation with TGF-β1 in GFP- and MAGP-2-expressing MB114 cells transiently transfected with either pHes1- or pSBE-luciferase, both together with pCMV-β-gal as indicated (data are the mean (±SEM) of 3 independent experiments; *, p<0.05; Student's T-Test).

FIG. 5A is a bar graph showing Hes-1 luciferase activity in MB114 cells transiently transfected with pHes1-luciferase and pCMV-β-gal cDNAs, incubated overnight in the absence or presence of DAPT (10 μM) (data are the mean (±SEM) of two independent experiments).

FIG. 5B is a bar graph showing endothelial angiogenic sprouting in quiescent MB114 cell monolayers induced to form angiogenic sprouts by addition of 10% FBS supplemented with or without DAPT (10 μM) (data are the mean (±SEM) of four independent experiment. (*, p<0.05; Student's T-Test)).

FIG. 5C is a bar graph showing Hes-1 luciferase activity in GFP-, MAGP-2-, and MAGP-2/N1ICD-expressing MB114 cells transiently transfected with pHes1-luciferase and pCMV-β-gal cDNAs (data are the mean (±SEM) of two independent experiments).

FIG. 5D is a bar graph showing endothelial angiogenic sprouting in quiescent monolayers of GFP-, MAGP-2-, and MAGP-2/N1ICD-expressing MB114 cells (bottom shows representative photomicrographs of angiogenic sprouts produced by GFP-, MAGP-2-, and MAGP-2N1ICD-expressing MB114 cells; data are the mean (±SEM) of four independent experiments; *, **, p<0.05; Student's T-Test).

FIG. 6 is a digitized image showing the time course of angiogenesis in vitro.

FIGS. 7A and 7B show retroviral expression of selected potential angiogenic proteins in MB114 cells via detergent-solubilized cell extracts (FIG. 7A) and semi-quantitative real-time PCR (FIG. 7B).

FIG. 8 is a digitized image showing that MAGP-2 is expressed aberrantly in a majority of human uterine tumors.

DETAILED DESCRIPTION OF THE INVENTION

The present invention generally relates to the discovery by the present inventor of several genes, and the proteins encoded thereby, that are associated with angiogenesis. More particularly, the present inventors used microarray analyses to monitor changes in the transcriptome of ECs undergoing angiogenesis when cultured onto tumor-derived basement membranes in vitro. In doing so, the inventors identified 308 genes whose expression was altered at least 3-fold during the angiogenic time course. Of these differentially-expressed genes, 63 encoded for EC secretory proteins and several were shown to mediate pro- or anti-angiogenic activities in vitro (e.g., SMOC-2, secreted MAGP-2 Promotes Angiogenesis modular calcium-binding protein-2; CRELD-2, cysteine-rich with EGF-like domains-1; MAGP-2, microfibril-associated glycoprotein-2; lumican; ECM-1, extracellular matrix protein-1). Expression of one of these genes, MAGP-2 (also known as Microfibrillar associated protein-5 (MFAP-5)), enhanced EC proliferation and p38 MAPK activation stimulated by bFGF, as well as stimulated EC invasion through synthetic basement membranes. The inventors have also demonstrated that MAGP-2 promoted EC sprouting in vitro, and as such, stimulated vessel formation and infiltration into Matrigel plugs implanted into genetically normal mice. Importantly, the inventors show herein that Notch1 activation prevented angiogenesis in vitro, a reaction that was overcome by MAGP-2-mediated antagonism of Notch1 signaling in ECs. Collectively, the inventors' findings have established MAGP-2 as a novel inducer of angiogenesis, doing so in part through its ability to antagonize Notch1 signaling in ECs. In addition, the inventors' findings have identified several additional targets for use in diagnostic, drug discovery and therapeutic applications related to the inhibition or promotion of angiogenesis.

More particularly, in order to increase the understanding of the role of ECs in mediating the remodeling of tumor and vascular microenvironments during pathological angiogenesis, the inventors cultured ECs on tumor-derived basement membranes to induce angiogenesis in vitro, and subsequently performed microarray analyses to identify alterations within the EC transcriptome that accompanied angiogenesis activation. In doing so, they focused specifically on genes that encoded secretory proteins or components of the ECM, which collectively comprised 20% (i.e., 63 out of 308 genes) of the differentially-expressed EC genes identified by the inventors (Table I). The analyses described herein also identified an additional 35 (˜11%) membrane-spanning and/or membrane-associated genes, whose expression and activation likely mediate paracrine and/or autocrine signaling in angiogenic ECs. Thus, secreted molecules constituted a significant fraction (˜31%) of all differentially regulated EC genes identified herein, thereby highlighting the importance of microenvironment remodeling during angiogenesis. The proportion of differentially-expressed EC genes classified as secretory proteins was similar to those observed in other recent EC transcriptome analyses (Aitkenhead et al, 2002; Bell et al, 2001; Kahn et al, 2000). However, unlike these profiling studies, the present inventors specifically investigated the inductive effect of tumor-derived basement membranes (i.e., Matrigel matrices) in regulating gene expression in tubulating ECs, and as such, numerous secretory proteins not previously associated with angiogenesis were identified (see Table I). Moreover, the inventors' identification of known angiogenic genes (Table I) validated this experimental design and gave credence to the notion that many of these newly identified genes may function as bone fide regulators of angiogenesis. Indeed, the present inventors' findings implicate ECM-1 and lumican as mediators of angiostasis, while CRELD-2 and SMOC-2 are proposed herein to function as novel mediators of angiogenesis (see discussion below). The ability of these EC secretory proteins to affect vessel development in vivo, as well as the molecular mechanisms whereby they mediate their pro- or anti-angiogenic activities in ECs can now be evaluated using the guidance provided herein.

An especially important finding of the present study was the inventors' identification of MAGP-2 as a novel mediator of angiogenesis. Indeed, the present inventors show for the first time that MAGP-2 expression stimulates EC proliferation, invasion, and angiogenic sprouting, as well as enhances EC activation of p38 MAPK in response to bFGF and EGF (FIG. 1). Moreover, MAGP-2 is shown to enhance the ability of bFGF to promote neovascularization and vessel infiltration into Matrigel plugs implanted into genetically normal mice (FIG. 2). Mechanistically, MAGP-2 is shown to induce angiogenesis through its ability to inhibit Notch1 processing and activation (FIGS. 3 and 4), an inhibitory reaction that is rescued by constitutive expression of Notch1 NICD (FIG. 5). Collectively, these findings have established MAGP-2 as a novel activator of angiogenesis, doing so in part via its ability to inhibit the Notch1 signaling pathway.

The precise mechanism whereby MAGP-2 antagonizes Notch1 signaling remains to be determined. Recent studies using heterologous cell expression systems have shown MAGP-2 to interact physically with Notch1 and its ligand, Jagged-1, resulting in their shedding from the cell surface (Miyamoto et al, 2006; Nehring et al, 2005). Although the inventors made no attempt to measure Notch1 and/or Jagged-1 extracellular domain shedding in response to MAGP-2, the production of such soluble Notch1 and Jagged-1 extracellular domains readily inhibits Notch signaling (Rebay et al, 1993; Small et al, 2001). In this fashion, MAGP-2 expression was observed to block the ability of Jagged-1 to stimulate Notch1 processing and the production of NICD, thereby preventing transactivation of the Hes1 promoter in ECs. Thus, MAGP-2 may promote angiogenesis in part by inducing Notch1 and/or Jagged-1 ectodomain shedding in ECs. In contrast to the present inventors' findings, Miyamoto et al (Miyamoto et al, 2006) recently found that MAGP-2 not only induces Notch1 ectodomain shedding in Cos-7 and NIH-3T3 cells, but also Notch1 processing and NICD production, leading to transcriptional activation of the Hes5 and CSL promoters. The reasons underlying this discrepancy are currently unknown, but most likely reflect differences in the cell types studied (i.e., ECs versus fibroblasts and kidney epithelial cells), as well as differences in microenvironmental factors that may influence the interactions between MAGP-2 and Notch1. In addition, cell-type specific expression of various Notch receptor and ligand combinations may also impact the ability of MAGP-2 to regulate, either positively or negatively, Notch signaling in responsive cells. Indeed, the present inventors, without being bound by theory, believe that MAGP-2 regulates angiogenesis in a context-specific manner via its ability to target both Notch signaling and elastin microfibril networks.

The present inventors' findings demonstrating the ability of MAGP-2 to stimulate angiogenesis by preventing Notch1 activation is intellectually credible in light of the established function of Notch in mediating angiostasis (Leong et al, 2002; Liu et al, 2006; Noseda et al, 2004; Williams et al, 2006; Zimrin et al, 1996). Moreover, the inventors recently observed MAGP-2 expression to be abnormally elevated in human uterine cancers (Example 6), and to significantly increase the growth and vascularization of MCA102 fibrosarcomas produced in mice (Albig and Schiemann, unpublished observation). It should be noted, however, that Notch activation also has been shown to stimulate angiogenesis (Leong and Karsan, 2005; Shawber and Kitajewski, 2004), and as such, it cannot yet be ascertained whether MAGP-2 promotes tumorigenesis by alleviating Notch1-mediated angiostasis, or by facilitating Notch1-mediated angiogenesis. The mechanisms whereby Notch mediates such disparate activities in ECs remains unclear, but may reflect a complex integration of cellular and environmental cues. Indeed, Notch signaling is subject to regulation by (i) the relative expression levels of various Notch receptors (Delaney et al, 2005; Duarte et al, 2004); (ii) the extent and form of Notch receptor glycosylation (Haines and Irvine, 2003); (iii) the availability of various Notch ligands within vascular microenvironments; and (iv) the activation of various Notch inhibitors, including MINT, Numb, NRARP, and proteolyzed ligands (Kadesch, 2004). The present inventors' findings herein and those by others (Miyamoto et al, 2006; Sakamoto et al, 2002) clearly show Notch signaling to be influenced by environmental cues, such as those produced by MAGP-2 (demonstrated herein).

Numerous additional EC secretory proteins were identified whose expression was also regulated by angiogenesis (Tables I and VI), suggesting that EC expression of these genes was obligatory for vessel development. Moreover, in vitro assays that modeled key steps in the angiogenic process showed that several these newly identified genes did indeed regulate EC activities-coupled to angiogenesis. For instance, lumican expression was found to inhibit MB114 cell proliferation (data not shown) and angiogenic sprouting (FIG. 1), as well as reduce the ability of bFGF and EGF to activate p38 MAPK in MB114 cells (FIG. 1). Lumican belongs the SLRP (small leucine-rich proteoglycan) family of ECM proteins, which also includes fibromodulin, biglycan, and the angiogenesis antagonist, decorin (Davies Cde et al, 2001; Kao et al, 2006; Sulochana et al, 2005). Genetic ablation of lumican in. mice indicates that this secreted proteoglycan functions in organizing collagen fibrils in the skin and cornea (Chakravarti et al, 1998). Additionally, lumican interacts physically with FasL (Fas-ligand), leading to enhanced Fas expression in and subsequent apoptosis of corneal fibroblasts (Vij et al, 2004; Vij et al, 2005). Recently, elevated lumican expression has been associated with cancers of the pancreas (Ping Lu et al, 2002), breast (Leygue et al, 1998), cervix (Naito et al, 2002), and colon (Lu et al, 2002), suggesting that lumican may promote tumorigenesis in these organs. In stark contrast, lumican expression also has been shown to inhibit the anchorage-independent growth and invasion of B16F1 melanoma cells in vitro, as well as their ability to form tumors in when implanted into mice (Vuillermoz et al, 2004). Thus, lumican also may function in suppressing cancer development and progression. Along these lines, the inventors have found that lumican antagonizes the development and infiltration of vessels in Matrigel plugs implanted into mice, as well as decreases the growth and blood vessel density of MCA102 fibrosarcomas produced in mice (Albig and Schiemann, unpublished observations).

The inventors further showed that ECM-1 is functionally similar to lumican and antagonized angiogenic sprouting by MB114 cells (FIG. 1). ECM-1 is a broadly distributed glycoprotein that plays important roles in maintaining normal skin structure, function, and homeostasis (Chan, 2004). In humans, loss of function mutations in ECM-1 elicit a rare genetic skin disease called lipoid proteinosis (Chan, 2004; Hamada et al, 2002), whose clinicopathological features are phenocopied in patients with lichen sclerosus, an acquired inflammatory disorder of the skin and mucous membranes associated with the development self-reactive ECM-1 antibodies (Oyama et al, 2003). Interestingly, both skin conditions are characterized by the (i) abnormal development of cutaneous microvessels, and (ii) excessive deposition of basement membrane proteins, leading to thickened mucous and vascular basement membranes (Kowalewski et al, 2005). ECM-1 overexpression is observed in cancers of the breast, esophagus, thyroid, stomach, and colon (Han et al, 2001; Kebebew et al, 2005; Wang et al, 2003), and has been associated with the acquisition of angiogenic (Han et al, 2001) and metastatic phenotypes (Wang et al, 2003). Thus, ECM-1 is an important regulator of basement membrane protein secretion and deposition, and quite possibly, of microenvironment remodeling (Kowalewski et al, 2005; Mirancea et al, 2006). As such, aberrant ECM-1 production likely dysregulates normal microenvironment conditions operant in balancing pro- and anti-angiogenic signals, leading to altered vessel formation and disease development in humans.

In contrast to lumican and ECM-1, the inventors observed CRELD-2 expression to significantly increase MB114 cell invasion, and to promote a trend towards enhanced angiogenic sprouting (FIG. 1), indicating that this secreted EGF-like domain containing protein may serve to enhance angiogenesis. Along these lines, the inventors found SMOC-2 expression to enhance the proliferative response of MB114 cells to bFGF, and more importantly, to increase MB114 cell invasion and angiogenic cell sprouting (FIG. 1). SMOC-2 and its related molecule, SMOC-1, are widely expressed glycoproteins that localize predominantly to basement membranes, and to various ECM structures (Vannahme et al, 2003; Vannahme et al, 2002). Structurally, SMOCs are defined by a unique, centrally located SMOC domain that is flanked N-terminally by follistatin-like and thyroglobulin-like domains, and C-terminally by an extracellular calcium-binding (EC) domain reminiscent of that found in SPARC (Vannahme et al, 2003; Vannahme et al, 2002). Interestingly, proteolytic cleavage of SPARC results in the release of biologically active fragments that can induce angiogenesis (Funk and Sage, 1993; Sage et al, 2003). SPARC, however, also mediates angiostasis by interacting physically with VEGF via its EC domain (Jendraschak and Sage, 1996; Kupprion et al, 1998). Thus, given the functional and structural similarities between SMOC-2 and SPARC, it remains to be determined whether SMOC-2 also mediates pro- and anti-angiogenic activities, and if so, whether these disparate EC activities occur via direct or indirect mechanisms.

Collectively, the inventors' findings indicate that lumican and EMC-1 function as novel angiogenesis antagonists, while CRELD-2 and SMOC-2 function as novel angiogenesis agonists. The molecular mechanisms underlying their ability to impact the activation or resolution of angiogenesis can now be determined.

The present invention more particularly relates to genes, nucleic acid molecules derived therefrom, and proteins or fragments thereof encoded by such genes and nucleic acid molecules, as well as homologues of such genes and proteins and related agents (e.g., antibodies, agonists, antagonists), and the use or targeting of such genes, nucleic acids, proteins, homologues and/or related agents, and/or compositions or formulations comprising the same, in methods related to the inhibition or promotion of angiogenesis, including the inhibition of angiogenesis for the inhibition or treatment of cancer. As discussed above, the present inventors identified 308 genes whose expression in angiogenic ECs was altered ≧3-fold. Of these differentially-expressed genes, 63 genes (˜20%) encoded EC secretory proteins (Table I), 35 genes (˜11%) encoded transmembrane or membrane-associated proteins (Table V), and 210 genes encoded non-secretory proteins (Table IV). This approach identified several secretory proteins that were previously known to be associated with angiogenesis and/or microenvironment remodeling, including ADAMTS1 (Iruela-Arispe et al, 2003), CTGF (Brigstock, 2002), HGF (Gao and Vande Woude, 2005), MMPs 3 and 9 (Heissig et al, 2003), thrombospondins 1 and 2 (Armstrong and Bornstein, 2003), and TIMP3 (Qi et al, 2003) (Table I, bold type face). In addition, the inventors identified numerous secretory proteins not previously associated with angiogenesis (e.g., Table I, regular text face), all of which are encompassed by the present invention. The inventors verified the differential expression of 19 individual genes by semi-quantitative real-time PCR (see Materials and Methods). These analyses showed significant concordance in the expression profiles measured either by real-time PCR or microarray analyses (Table VI), indicating that these (and other) genes are indeed bona fide targets of angiogenic signaling systems in tubulating ECs.

Accordingly genes that are encompassed by the present invention (as well as nucleic acid molecules derived from or comprising at least a portion of the coding region and/or regulatory region of such genes and any proteins or fragments thereof encoded by such genes) include any of the genes or portions of genes (including ESTs) represented in Table I, Table IV, Table V, and/or Table VI. Preferred genes for use in the present invention include any of the genes presented in regular (non-bold)-type face in Table I or Table V and/or any of the genes in Table VI. The invention also includes the use of nucleic acid molecules derived from or comprising at least a portion of the coding region and/or regulatory region of such genes and any proteins or fragments thereof encoded by such genes. Particularly preferred genes for use in the present invention include any of the genes in Table VI. The invention also includes the use of nucleic acid molecules derived from or comprising at least a portion of the coding region and/or regulatory region of such genes and any proteins or fragments thereof encoded by such genes.

In one embodiment, the invention includes the use of genes encoding any one or more of the following proteins, the genes or nucleic acid sequences therein, or primers used to amplify and identify such genes being identified in Table I and/or Table III and/or Table VI:

murine ADAMts7 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. AL359939),

human ADAMts7 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. AF140675),

murine CRELD-2 or the human equivalent thereof (murine CRELD-2 encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. AK017880),

murine Decorin (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. NM_(—)007833),

human Decorin (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. AH002681),

murine ECM1 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. NM_(—)007899),

human ECM1 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. NP_(—)001415),

murine Inhibin β-b (encoded by a gene comprising the nucleic acid sequence represented herein by SEQ ID NO:97 or SEQ ID NO:98)

human Inhibin β-b (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. NM_(—)002193),

murine Integrin α-3 (encoded by a gene comprising the nucleic acid sequence represented herein by SEQ ID NO:99 or SEQ ID NO:100),

human Integrin α-3 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. E16082),

murine Integrin α-6 (encoded by a gene comprising the nucleic acid sequence represented herein by SEQ ID NO:101 or SEQ ID NO:102),

human Integrin α-6 (encoded by a gene comprising the nucleic acid sequence found in, for example, GenBank Accession No. AH008066),

murine Lipocalin-7 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. BC005738 and represented herein by SEQ ID NO:103 or SEQ ID NO:104),

human Lipocalin-7 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. NM_(—)022164),

murine Loxl-3 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. NM_(—)013586, the amino acid sequence encoded by which is represented herein by SEQ ID NO:40),

human Loxl-3 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. AAH71865, the amino acid sequence encoded by which is represented herein by SEQ ID NO:41),

murine Lumican (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. AK014312),

human Lumican (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. AF239660),

murine MAGP-2 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. NM_(—)015776 and represented herein by SEQ ID NO:123, the amino acid sequence encoded by which is represented herein by SEQ ID NO:42),

human MAGP-2 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. AAC83942 and represented herein by SEQ ID NO:124, the amino acid sequence encoded by which is represented herein by SEQ ID NO:43),

murine Matrilin-2 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. BC005429),

human Matrilin-2 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. BC010444),

murine Nephronectin (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. AA223007 the amino acid sequence encoded by which is represented herein by SEQ ID NO:52),

human Nephronectin (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. NM_(—)001033047, the amino acid sequence encoded by which is represented herein by SEQ ID NO:53),

murine SerpinE2 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. NM_(—)009255),

human SerpinE2 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. BC042628),

murine SMOC-2 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. NM_(—)022315), and

human SMOC-2 (encoded by a gene comprising the nucleic acid sequence found in GenBank Accession No. NM_(—)022138).

The invention also includes the use of nucleic acid molecules derived from or comprising at least a portion of the coding region and/or regulatory region of such genes and any proteins or fragments thereof encoded by such genes, as well as agonists and antagonists of any of such proteins or genes.

In another embodiment, the invention includes the use of genes from Table V encoding any one or more of the following proteins:

murine 0610007C21Rik (GenBank Accession No. AK002276; encoding a protein represented herein by SEQ ID NO:1);

human apoptosis related protein APR-3 (GenBank Accession No. AF144055; encoding a protein represented herein by SEQ ID NO:2);

murine 1810014L12Rik (GenBank Accession No. NM_(—)133706; encoding a protein represented herein by SEQ ID NO:3);

human 1810014L12Rik (GenBank Accession No. NP_(—)055388; encoding a protein represented herein by SEQ ID NO:4);

murine Cd14 (GenBank Accession No. NM_(—)009841; encoding CD14 antigen represented herein by SEQ ID NO:5);

human Cd14 (GenBank Accession No. NP_(—)000638; encoding CD14 antigen represented herein by SEQ ID NO:6);

murine Cd38 (GenBank Accession No. BB256012; comprising a nucleic acid sequence represented herein by SEQ ID NO:7 and encoding CD38 antigen);

murine Cd53 (GenBank Accession No. NM_(—)007651; encoding CD53 antigen represented herein by SEQ ID NO:8);

human Cd53 (GenBank Accession No. NP_(—)000551; encoding CD53 antigen represented herein by SEQ ID NO:9);

murine Emp2 (GenBank Accession No. AF083076; encoding epithelial membrane protein represented herein by SEQ ID NO:10);

human Emp2 (GenBank Accession No. NP_(—)001415; encoding epithelial membrane protein represented herein by SEQ ID NO:11);

murine Fcgrt (GenBank Accession No. NM_(—)010189; encoding Fc receptor (IgG, alpha chain transporter) represented herein by SEQ ID NO:12);

human Fcgrt (GenBank Accession No. NP_(—)004098; encoding Fc receptor (IgG, alpha chain transporter) represented herein by SEQ ID NO:13);

murine Islr (GenBank Accession No. NM_(—)012043; encoding immunoglobulin superfamily containing leucine-rich repeat represented herein by SEQ ID NO:14);

human Islr (GenBank Accession No. NP_(—)005536; encoding immunoglobulin superfamily containing leucine-rich repeat represented herein by SEQ ID NO:15);

murine Lrp2 (GenBank Accession No. C80829; comprising a nucleic acid sequence represented herein by SEQ ID NO:16 and encoding low density lipoprotein receptor-related protein 2);

human Lrp2 (GenBank Accession No. NP_(—)004516; comprising a nucleic acid sequence represented herein by SEQ ID NO:17 and encoding low density lipoprotein receptor-related protein 2);

murine Ly6a (GenBank Accession No. BC002070; encoding lymphocyte antigen 6 complex, locus A represented herein by SEQ ID NO:18);

murine P2rx4 (GenBank Accession No. AJ251462; encoding purinergic receptor P2X, ligand-gated ion channel 4, represented herein by SEQ ID NO:19);

human P2rx4 (GenBank Accession No. Q99571; encoding purinergic receptor P2X, ligand-gated ion channel 4, represented herein by SEQ ID NO:20);

murine Pcdhb9 (GenBank Accession No. NM_(—)053134; encoding protocadherin beta 9 represented herein by SEQ ID NO:21);

human Pcdhb9 (GenBank Accession No. AA103495; encoding protocadherin beta 9 represented herein by SEQ ID NO:22);

murine Ptpre (GenBank Accession No. U35368; encoding protein tyrosine phosphatase receptor type E represented herein by SEQ ID NO:23);

human Ptpre (GenBank Accession No. NP_(—)569119; encoding protein tyrosine phosphatase receptor type E represented herein by SEQ ID NO:24);

murine Slc4a3 (GenBank Accession No. NM_(—)009208; encoding solute carrier family 4 (anion exchanger) member 3, represented herein by SEQ ID NO:25);

human Slc4a3 (GenBank Accession No. NP_(—)005061; encoding solute carrier family 4 (anion exchanger) member 3, represented herein by SEQ ID NO:26);

murine Tmc6 (GenBank Accession No. BC004840; encoding transmembrane channel-like gene family 6 represented herein by SEQ ID NO:27).

and/or human Tmc6 (GenBank Accession No. AAH35648; encoding transmembrane channel-like gene family 6 represented herein by SEQ ID NO:28).

The invention also includes the use of nucleic acid molecules derived from or comprising at least a portion of the coding region and/or regulatory region of such genes and any proteins or fragments thereof encoded by such genes, as well as agonists and antagonists of any of such proteins or genes.

In another embodiment, the invention includes the use of genes from Table I encoding any one or more of the following proteins:

murine 9130213B05Rik (GenBank Accession No. BC006604; encoding a protein represented herein by SEQ ID NO:29);

murine C1s (GenBank Accession No. BC022123; encoding complement component 1, s subcomponent, represented herein by SEQ ID NO:34);

human C1s (GenBank Accession No. NM_(—)001734; encoding complement component 1, s subcomponent, represented herein by SEQ ID NO:35);

murine C3 (GenBank Accession No. K02782; encoding complement component 3 represented herein by SEQ ID NO:30);

human C3 (GenBank Accession No. NP_(—)000055; encoding complement component 3 represented herein by SEQ ID NO:31);

murine Cfh (GenBank Accession No. AI987976; comprising a nucleic acid sequence represented herein by SEQ ID NO:32 and encoding complement component factor h);

human Cfh (GenBank Accession No. CAA30403; comprising a nucleic acid sequence represented herein by SEQ ID NO:33 and encoding complement component factor h);

murine Col9a3 (GenBank Accession No. BG074456; comprising a nucleic acid sequence represented herein by SEQ ID NO:36 and encoding procollagen, type IX, alpha 3);

human Col9a3 (GenBank Accession No. Q14050; comprising a nucleic acid sequence represented herein by SEQ ID NO:37 and encoding procollagen, type IX, alpha 3);

murine Grem1 (GenBank Accession No. BC015293; encoding cysteine knot superfamily 1, BMP antagonist 1, represented herein by SEQ ID NO:38);

human Grem1 (GenBank Accession No. NP_(—)037504; encoding cysteine knot superfamily 1, BMP antagonist 1, represented herein by SEQ ID NO:39);

murine Loxl3 (GenBank Accession No. NM_(—)013586; encoding lysyl oxidase-like 3, represented herein by SEQ ID NO:40);

human Loxl3 (GenBank Accession No. AAH71865; encoding lysyl oxidase-like 3, represented herein by SEQ ID NO:41);

murine MAGP-2 (GenBank Accession No. NM_(—)015776; comprising a nucleic acid sequence represented herein by SEQ ID NO:123 and encoding microfibril-associated glycoprotein-2 (also known as microfibrillar associated protein 5), represented herein by SEQ ID NO:42);

human MAGP-2 (GenBank Accession No. AAC83942; comprising a nucleic acid sequence represented herein by SEQ ID NO:124 and encoding microfibrillar associated protein 5, represented herein by SEQ ID NO:43);

murine Mglap (GenBank Accession No. NM_(—)008597; encoding matrix gamma-carboxyglutamate (gla) protein represented herein by SEQ ID NO:44);

human Mglap (GenBank Accession No. AAP36640; encoding matrix gamma-carboxyglutamate (gla) protein represented herein by SEQ ID NO:45);

murine Naga (GenBank Accession No. BC021631; encoding N-acetyl galactosaminidase, alpha, represented herein by SEQ ID NO:46);

human Naga (GenBank Accession No. NP_(—)000253; encoding N-acetyl galactosaminidase, alpha, represented herein by SEQ ID NO:47);

murine Nbl1 (GenBank Accession No. NM_(—)008675; encoding neuroblastoma, suppression of tumorigenicity 1, represented herein by SEQ ID NO:48);

human Nbl1 (GenBank Accession No. AAL15440; encoding neuroblastoma, suppression of tumorigenicity 1, represented herein by SEQ ID NO:49);

murine Ngfb (GenBank Accession No. NM_(—)013609; encoding nerve growth factor, beta, represented herein by SEQ ID NO:50);

human Ngfb (GenBank Accession No. AAH32517; encoding nerve growth factor, beta, represented herein by SEQ ID NO:51);

murine Npnt (GenBank Accession No. AA223007; encoding nephronectin and represented herein by SEQ ID NO:52);

human Npnt (GenBank Accession No. NM_(—)001033047; encoding nephronectin and represented herein by SEQ ID NO:53);

murine Olfm1 (GenBank Accession No. C78264; encoding olfactomedin 1, represented herein by SEQ ID NO:54);

human Olfm1 (GenBank Accession No. Q99784; encoding olfactomedin 1, represented herein by SEQ ID NO:55);

and/or murine U90926 (GenBank Accession No. NM_(—)020562; encoding a protein represented herein by SEQ ID NO:56).

The invention also includes the use of nucleic acid molecules derived from or comprising at least a portion of the coding region and/or regulatory region of such genes and any proteins or fragments thereof encoded by such genes.

The genes identified in the Tables herein are identified by name, by GenBank Accession numbers, and by description of the protein, when available. The amino acid sequence for several of the proteins encoded by the genes in the Tables herein are also provided herein. All information associated with the publicly available identifiers and accession numbers in any of the tables described herein, including the nucleic acid sequences of the genes and probes and the amino acid sequences of the proteins encoded thereby, is incorporated herein by reference in its entirety.

Genes and proteins identified in the present invention can also be referred to as “biomarkers”. The term “biomarker” as used herein can refer to gene described herein or to the protein encoded by that gene, wherein the gene has been identified as being differentially regulated during angiogenesis. In addition, the term “biomarker” can be generally used to refer to any portion of such a gene or protein that can identify or correlate with the full-length gene or protein, for example, in an assay or other method of the invention.

Microfibril-associated glycoprotein-2 (MAGP-2) is a secreted glycoprotein (25 kDa) that incorporates into and organizes elastin fibril networks by interacting with tropoelastin, and with fibrillins 1 and 2; it also mediates cell adhesion by ligating integrins via its RGD integrin-binding motif (Gibson et al, 1998; Gibson et al, 1999). Abnormally elevated MAGP-2 expression is observed in the skin of systemic sclerosis patients, as well as in mouse models of systemic sclerosis that have associated MAGP-2 expression with excessive matrix deposition of type I collagen (Lemaire et al, 2004; Lemaire et al, 2005). Moreover, skin lesions in systemic sclerosis patients contain aberrant vessel morphologies characteristic of abnormal angiogenesis (Bodolay et al, 2002). In addition, MAGP-2 expression is induced in human T-47DE3 breast cancer cells when treated with progestin (Graham et al, 2005), and in human A549 lung adenocarcinoma cells when implanted into nude mice (Creighton et al, 2003). Most recently, MAGP-2 has been shown to interact physically with Notch1 (Miyamoto et al, 2006) and its ligand, Jagged-1 (Nehring et al, 2005), leading to the ectodomain shedding of both molecules from the cell surface.

Human MAGP-2 cDNA has been cloned and described, for example, in Faraco et al. (Genomics. 1995 Feb. 10; 25(3):630-7) and in Gibson et al. (J Biol Chem. 1996 Jan. 12; 271(2):1096-103). The organization of the human MAGP-2 gene is described in Hatzinikolas and Gibson (J Biol Chem. 1998 Nov. 6; 273(45):29309-14). The organization of the mouse MAGP-2 gene has been described by Frankfater et al. (Mamm Genome. 2000 Mar.; 11(3):191-5). The nucleotide sequence encoding human MAGP-2 is described in the National Center for Biotechnology Information (NCBI) database Accession No. AH007047 (gi:3983462) and is represented herein by SEQ ID NO:124. The amino acid sequence for human MAGP-2 is represented herein as SEQ ID NO:43 and is also found in the NCBI database Accession No. AAC83942 (gi:3983463). The nucleotide sequences encoding bovine and murine MAGP-2 are also known. The nucleotide sequence encoding murine MAGP-2 is described in NCBI database Accession No. BC025131 (gi: 19264044) and is represented herein by SEQ ID NO:123 and encodes the murine MAGP-2 protein, described in NCBI database Accession No. AAH25131 (gi:19264045), also represented herein by SEQ ID NO:42. The nucleotide sequence encoding bovine MAGP-2 is described in NCBI database Accession No. NM_(—)174386 (gi:31342148) and encodes the bovine MAGP-2 protein, described in NCBI database Accession No. NP_(—)776811 (gi:27805993). All of the information contained in the database accession numbers and in the publications referenced herein is incorporated herein by reference.

In accordance with the present invention, an isolated polynucleotide (also referred to as an isolated nucleic acid molecule) is a nucleic acid molecule that has been removed from its natural milieu (e.g., that has been subject to human manipulation), its natural milieu being the genome or chromosome in which the nucleic acid molecule is found in nature. As such, “isolated” does not necessarily reflect the extent to which the nucleic acid molecule has been purified, but indicates that the molecule does not include an entire genome or an entire chromosome in which the nucleic acid molecule is found in nature. The polynucleotides useful in the present invention are typically a portion of a gene (sense or non-sense strand) of the present invention that is suitable for use as a hybridization probe or PCR primer for the identification of a full-length gene (or portion thereof) in a given sample, to encode a protein or fragment thereof, or as a therapeutic reagent (e.g., antisense). An isolated nucleic acid molecule can include a gene or a portion of a gene (e.g., the regulatory region or promoter), for example, to produce a reporter construct according to the present invention. An isolated nucleic acid molecule that includes a gene is not a fragment of a chromosome that includes such gene, but rather includes the coding region and regulatory regions associated with the gene, but no additional genes naturally found on the same chromosome. An isolated nucleic acid molecule can also include a specified nucleic acid sequence flanked by (i.e., at the 5′ and/or the 3′ end of the sequence) additional nucleic acids that do not normally flank the specified nucleic acid sequence in nature (i.e., heterologous sequences). Isolated nucleic acid molecule can include DNA, RNA (e.g., mRNA), or derivatives of either DNA or RNA (e.g., cDNA). Although the phrase “nucleic acid molecule” primarily refers to the physical nucleic acid molecule and the phrase “nucleic acid sequence” primarily refers to the sequence of nucleotides on the nucleic acid molecule, the two phrases can be used interchangeably, especially with respect to a nucleic acid molecule, or a nucleic acid sequence, being capable of encoding a protein. Preferably, an isolated nucleic acid molecule of the present invention is produced using recombinant DNA technology (e.g., polymerase chain reaction (PCR) amplification, cloning) or chemical synthesis.

The minimum size of a nucleic acid molecule or polynucleotide of the present invention is a size sufficient to encode a protein having a desired biological activity, sufficient to form a probe or oligonucleotide primer that is capable of forming a stable hybrid with the complementary sequence of a nucleic acid molecule encoding the natural protein (e.g., under moderate, high or very high stringency conditions), or to otherwise be used as a target or agent in an assay or in any therapeutic method discussed herein. If the polynucleotide is an oligonucleotide probe or primer, the size of the polynucleotide can be dependent on nucleic acid composition and percent homology or identity between the nucleic acid molecule and a complementary sequence as well as upon hybridization conditions per se (e.g., temperature, salt concentration, and formamide concentration). The minimum size of a polynucleotide that is used as an oligonucleotide probe or primer is at least about 5 nucleotides in length, and preferably ranges from about 5 to about 50 or about 500 nucleotides or greater (1000, 2000, etc.), including any length in between, in whole number increments (i.e., 5, 6, 7, 8, 9, 10, . . . 33, 34, . . . 256, 257, . . . 500 . . . 1000 . . . ), and more preferably from about 10 to about 40 nucleotides, and most preferably from about 15 to about 40 nucleotides in length. In one aspect, the oligonucleotide primer or probe is typically at least about 12 to about 15 nucleotides in length if the nucleic acid molecules are GC-rich and at least about 15 to about 18 bases in length if they are AT-rich. There is no limit, other than a practical limit, on the maximal size of a nucleic acid molecule of the present invention, in that the nucleic acid molecule can include a portion of a protein-encoding sequence or a nucleic acid sequence encoding a full-length protein.

According to the present invention, an oligonucleotide probe (or simply, probe) is a nucleic acid molecule which most typically ranges in size from about 8 nucleotides to several hundred nucleotides in length. Such a molecule is typically used to identify a target nucleic acid sequence in a sample by hybridizing to such target nucleic acid sequence under stringent hybridization conditions. As used herein, stringent hybridization conditions refer to standard hybridization conditions under which nucleic acid molecules are used to identify similar nucleic acid molecules. Such standard conditions are disclosed, for example, in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Labs Press, 1989. Sambrook et al., ibid., is incorporated by reference herein in its entirety (see specifically, pages 9.31-9.62). In addition, formulae to calculate the appropriate hybridization and wash conditions to achieve hybridization permitting varying degrees of mismatch of nucleotides are disclosed, for example, in Meinkoth et al., 1984, Anal. Biochem. 138, 267-284; Meinkoth et al., ibid., is incorporated by reference herein in its entirety.

More particularly, moderate stringency hybridization and washing conditions, as referred to herein, refer to conditions which permit isolation of nucleic acid molecules having at least about 70% nucleic acid sequence identity with the nucleic acid molecule being used to probe in the hybridization reaction (i.e., conditions permitting about 30% or less mismatch of nucleotides). High stringency hybridization and washing conditions, as referred to herein, refer to conditions which permit isolation of nucleic acid molecules having at least about 80% nucleic acid sequence identity with the nucleic acid molecule being used to probe in the hybridization reaction (i.e., conditions permitting about 20% or less mismatch of nucleotides). Very high stringency hybridization and washing conditions, as referred to herein, refer to conditions which permit isolation of nucleic acid molecules having at least about 90% nucleic acid sequence identity with the nucleic acid molecule being used to probe in the hybridization reaction (i.e., conditions permitting about 10% or less mismatch of nucleotides). As discussed above, one of skill in the art can use the formulae in Meinkoth et al., ibid. to calculate the appropriate hybridization and wash conditions to achieve these particular levels of nucleotide mismatch. Such conditions will vary, depending on whether DNA:RNA or DNA:DNA hybrids are being formed. Calculated melting temperatures for DNA:DNA hybrids are 10° C. less than for DNA:RNA hybrids. In particular embodiments, stringent hybridization conditions for DNA:DNA hybrids include hybridization at an ionic strength of 6×SSC (0.9 M Na⁺) at a temperature of between about 20° C. and about 35° C. (lower stringency), more preferably, between about 28° C. and about 40° C. (more stringent), and even more preferably, between about 35° C. and about 45° C. (even more stringent), with appropriate wash conditions. In particular embodiments, stringent hybridization conditions for DNA:RNA hybrids include hybridization at an ionic strength of 6×SSC (0.9 M Na⁺) at a temperature of between about 30° C. and about 45° C., more preferably, between about 38° C. and about 50° C., and even more preferably, between about 45° C. and about 55° C., with similarly stringent wash conditions. These values are based on calculations of a melting temperature for molecules larger than about 100 nucleotides, 0% formamide and a G+C content of about 40%. Alternatively, T_(m) can be calculated empirically as set forth in Sambrook et al., supra, pages 9.31 to 9.62. In general, the wash conditions should be as stringent as possible, and should be appropriate for the chosen hybridization conditions. For example, hybridization conditions can include a combination of salt and temperature conditions that are approximately 20-25° C. below the calculated T_(m) of a particular hybrid, and wash conditions typically include a combination of salt and temperature conditions that are approximately 12-20° C. below the calculated T_(m) of the particular hybrid. One example of hybridization conditions suitable for use with DNA:DNA hybrids includes a 2-24 hour hybridization in 6×SSC (50% formamide) at about 42° C., followed by washing steps that include one or more washes at room temperature in about 2×SSC, followed by additional washes at higher temperatures and lower ionic strength (e.g., at least one wash as about 37° C. in about 0.1×-0.5×SSC, followed by at least one wash at about 68° C. in about 0.1×-0.5×SSC).

PCR primers are also nucleic acid sequences, although PCR primers are typically oligonucleotides of fairly short length that are used in polymerase chain reactions. PCR primers and hybridization probes can readily be developed and produced by those of skill in the art, using sequence information from the target sequence. (See, for example, Sambrook et al., supra or Glick et al., supra).

Knowing the nucleic acid sequences of certain nucleic acid molecules of the present invention allows one skilled in the art to, for example, (a) make copies of those nucleic acid molecules and/or (b) obtain nucleic acid molecules including at least a portion of such nucleic acid molecules (e.g., nucleic acid molecules including full-length genes, full-length coding regions, regulatory control sequences, truncated coding regions). Such nucleic acid molecules can be obtained in a variety of ways including traditional cloning techniques using oligonucleotide probes to screen appropriate libraries or DNA and PCR amplification of appropriate libraries or DNA using oligonucleotide primers. Preferred libraries to screen or from which to amplify nucleic acid molecule include mammali7an genomic DNA libraries. Techniques to clone and amplify genes are disclosed, for example, in Sambrook et al., ibid.

As used herein, reference to an isolated protein or polypeptide in the present invention, including any of the proteins described particularly herein (e.g., any protein encoded by a gene or nucleic acid sequence referenced in Table I, Table IV, Table V, and/or Table VI), includes full-length proteins, fusion proteins, or any fragment or homologue of such a protein. Such a protein can include, but is not limited to, purified proteins, recombinantly produced proteins, membrane bound proteins, proteins complexed with lipids, soluble proteins and isolated proteins associated with other proteins. More specifically, an isolated protein, such as a MAGP-2 (MFAP-5) protein, by way of example, according to the present invention, is a protein (including a polypeptide or peptide) that has been removed from its natural milieu (i.e., that has been subject to human manipulation) and can include purified proteins, partially purified proteins, recombinantly produced proteins, and synthetically produced proteins, for example. As such, “isolated” does not reflect the extent to which the protein has been purified. Preferably, an isolated protein of the present invention is produced recombinantly. In addition, and again by way of example, a “human MAGP-2 protein” or a protein “derived from” a human MAGP-2 protein refers to a MAGP-2 protein (generally including a homologue of a naturally occurring MAGP-2 protein) from a human (Homo sapiens) or to a MAGP-2 protein that has been otherwise produced from the knowledge of the structure (e.g., sequence) and perhaps the function of a naturally occurring MAGP-2 protein from Homo sapiens. In other words, a human MAGP-2 protein includes any MAGP-2 protein that has substantially similar structure and function of a naturally occurring MAGP-2 protein from Homo sapiens or that is a biologically active (i.e., has biological activity) homologue of a naturally occurring MAGP-2 protein from Homo sapiens as described in detail herein. As such, a human MAGP-2 protein can include purified, partially purified, recombinant, mutated/modified and synthetic proteins. According to the present invention, the terms “modification” and “mutation” can be used interchangeably, particularly with regard to the modifications/mutations to the amino acid sequence of protein (or nucleic acid sequences) described herein. An isolated protein useful as an antagonist or agonist according to the present invention can be isolated from its natural source, produced recombinantly or produced synthetically.

As used herein, the term “homologue” is used to refer to a protein or peptide which differs from a naturally occurring protein or peptide (i.e., the “prototype” or “wild-type” protein) by minor modifications to the naturally occurring protein or peptide, but which maintains the basic protein and side chain structure of the naturally occurring form. Such changes include, but are not limited to: changes in one or a few amino acid side chains; changes one or a few amino acids, including deletions (e.g., a truncated version of the protein or peptide) insertions and/or substitutions; changes in stereochemistry of one or a few atoms; and/or minor derivatizations, including but not limited to: methylation, glycosylation, phosphorylation, acetylation, myristoylation, prenylation, palmitation, amidation and/or addition of glycosylphosphatidyl inositol. A homologue can have either enhanced, decreased, or substantially similar properties as compared to the naturally occurring protein or peptide. A homologue can include an agonist of a protein or an antagonist of a protein.

Homologues can be the result of natural allelic variation or natural mutation. A naturally occurring allelic variant of a nucleic acid encoding a protein is a gene that occurs at essentially the same locus (or loci) in the genome as the gene which encodes such protein, but which, due to natural variations caused by, for example, mutation or recombination, has a similar but not identical sequence. Allelic variants typically encode proteins having similar activity to that of the protein encoded by the gene to which they are being compared. One class of allelic variants can encode the same protein but have different nucleic acid sequences due to the degeneracy of the genetic code. Allelic variants can also comprise alterations in the 5′ or 3′ untranslated regions of the gene (e.g., in regulatory control regions). Allelic variants are well known to those skilled in the art.

Homologues can be produced using techniques known in the art for the production of proteins including, but not limited to, direct modifications to the isolated, naturally occurring protein, direct protein synthesis, or modifications to the nucleic acid sequence encoding the protein using, for example, classic or recombinant DNA techniques to effect random or targeted mutagenesis.

According to the present invention, an isolated protein, including a biologically active homologue or fragment thereof, has at least one characteristic of biological activity of activity the wild-type, or naturally occurring reference protein (which can vary depending on whether the homologue or fragment is an agonist or antagonist of the protein, or whether an agonist or antagonist mimetic of the protein is described). In general, the biological activity or biological action of a protein refers to any function(s) exhibited or performed by the protein that is ascribed to the naturally occurring form of the protein as measured or observed in vivo (i.e., in the natural physiological environment of the protein) or in vitro (i.e., under laboratory conditions). Modifications, activities or interactions which result in a decrease in protein expression or a decrease in the activity of the protein, can be referred to as inactivation (complete or partial), down-regulation, reduced action, or decreased action or activity of a protein. Similarly, modifications, activities or interactions which result in an increase in protein expression or an increase in the activity of the protein, can be referred to as amplification, overproduction, activation, enhancement, up-regulation or increased action of a protein. The biological activity of a protein according to the invention can be measured or evaluated using any assay for the biological activity of the protein as known in the art. Such assays can include, but are not limited to, binding assays, assays to determine internalization of the protein and/or associated proteins, enzyme assays, cell signal transduction assays (e.g., phosphorylation assays), and/or assays for determining downstream cellular events that result from activation or binding of the cell surface protein (e.g., expression of downstream genes, production of various biological mediators, etc.).

As used herein, reference to an “agonist” of a given protein refers to any compound that is characterized by the ability to agonize (e.g., stimulate, induce, increase, enhance, or mimic) the biological activity of the naturally occurring protein, and includes any homologue, binding protein (e.g., an antibody), agent that interacts with a protein or receptor bound by the protein, or any suitable product of drug/compound/peptide design or selection which is characterized by its ability to agonize (e.g., stimulate, induce, increase, enhance) the biological activity of the naturally occurring protein in a manner similar to the natural agonist, which is the reference protein.

Similarly, reference to an “antagonist” refers to any compound which inhibits (e.g., antagonizes, reduces, decreases, blocks, reverses, or alters) the effect of a given agonist of a protein (including the protein itself) as described above. More particularly, an antagonist is capable of acting in a manner relative to the activity of the protein, such that the biological activity of the natural agonist or reference protein, is decreased in a manner that is antagonistic (e.g., against, a reversal of, contrary to) to the natural action of the protein. Such antagonists can include, but are not limited to, a protein, peptide, or nucleic acid (including ribozymes, RNAi, aptamers, and antisense), antibodies and antigen binding fragments thereof, or product of drug/compound/peptide design or selection that provides the antagonistic effect.

As used herein, an anti-sense nucleic acid molecule is defined as an isolated nucleic acid molecule that reduces expression of a protein by hybridizing under high stringency conditions to a gene encoding the protein. Such a nucleic acid molecule is sufficiently similar to the gene encoding the protein that the molecule is capable of hybridizing under high stringency conditions to the coding or complementary strand of the gene or RNA encoding the natural protein. RNA interference (RNAi) is a process whereby double stranded RNA, and in mammalian systems, short interfering RNA (siRNA), is used to inhibit or silence expression of complementary genes. In the target cell, siRNA are unwound and associate with an RNA induced silencing complex (RISC), which is then guided to the mRNA sequences that are complementary to the siRNA, whereby the RISC cleaves the mRNA. A ribozyme is an RNA segment that functions by binding to the target RNA moiety and inactivate it by cleaving the phosphodiester backbone at a specific cutting site. A ribozyme can serve as a targeting delivery vehicle for a nucleic acid molecule, or alternatively, the ribozyme can target and bind to RNA encoding the biomarker, for example, and thereby effectively inhibit the translation of the biomarker. Aptamers are short strands of synthetic nucleic acids (usually RNA but also DNA) selected from randomized combinatorial nucleic acid libraries by virtue of their ability to bind to a predetermined specific target molecule with high affinity and specificity. Aptamers assume a defined three-dimensional structure and are capable of discriminating between compounds with very small differences in structure.

Homologues of a given protein, including peptide and non-peptide agonists and antagonists (analogs), can be products of drug design or selection and can be produced using various methods known in the art. Such homologues can be referred to as mimetics. Various methods of drug design, useful to design or select mimetics or other therapeutic compounds useful in the present invention are disclosed in Maulik et al., 1997, Molecular Biotechnology: Therapeutic Applications and Strategies, Wiley-Liss, Inc., which is incorporated herein by reference in its entirety.

As used herein, a mimetic refers to any peptide or non-peptide compound that is able to mimic the biological action of a naturally occurring peptide, often because the mimetic has a basic structure that mimics the basic structure of the naturally occurring peptide and/or has the salient biological properties of the naturally occurring peptide. Mimetics can include, but are not limited to: peptides that have substantial modifications from the prototype such as no side chain similarity with the naturally occurring peptide (such modifications, for example, may decrease its susceptibility to degradation); anti-idiotypic and/or catalytic antibodies, or fragments thereof; non-proteinaceous portions of an isolated protein (e.g., carbohydrate structures); or synthetic or natural organic molecules, including nucleic acids and drugs identified through combinatorial chemistry, for example. Such mimetics can be designed, selected and/or otherwise identified using a variety of methods known in the art.

A mimetic can be obtained, for example, from molecular diversity strategies (a combination of related strategies allowing the rapid construction of large, chemically diverse molecule libraries), libraries of natural or synthetic compounds, in particular from chemical or combinatorial libraries (i.e., libraries of compounds that differ in sequence or size but that have the similar building blocks) or by rational, directed or random drug design. See for example, Maulik et al., supra.

In a molecular diversity strategy, large compound libraries are synthesized, for example, from peptides, oligonucleotides, carbohydrates and/or synthetic organic molecules, using biological, enzymatic and/or chemical approaches. The critical parameters in developing a molecular diversity strategy include subunit diversity, molecular size, and library diversity. The general goal of screening such libraries is to utilize sequential application of combinatorial selection to obtain high-affinity ligands for a desired target, and then to optimize the lead molecules by either random or directed design strategies. Methods of molecular diversity are described in detail in Maulik, et al., ibid.

In a rational drug design procedure, the three-dimensional structure of a regulatory compound can be analyzed by, for example, nuclear magnetic resonance (NMR) or X-ray crystallography. This three-dimensional structure can then be used to predict structures of potential compounds, such as potential regulatory agents by, for example, computer modeling. The predicted compound structure can be used to optimize lead compounds derived, for example, by molecular diversity methods. In addition, the predicted compound structure can be produced by, for example, chemical synthesis, recombinant DNA technology, or by isolating a mimetope from a natural source (e.g., plants, animals, bacteria and fungi).

Maulik et al. also disclose, for example, methods of directed design, in which the user directs the process of creating novel molecules from a fragment library of appropriately selected fragments; random design, in which the user uses a genetic or other algorithm to randomly mutate fragments and their combinations while simultaneously applying a selection criterion to evaluate the fitness of candidate ligands; and a grid-based approach in which the user calculates the interaction energy between three dimensional receptor structures and small fragment probes, followed by linking together of favorable probe sites.

In one embodiment, a homologue of a given protein comprises, consists essentially of, or consists of, an amino acid sequence that is at least about 45%, or at least about 50%, or at least about 55%, or at least about 60%, or at least about 65%, or at least about 70%, or at least about 75%, or at least about 80%, or at least about 85%, or at least about 90%, or at least about 95% identical, or at least about 95% identical, or at least about 96% identical, or at least about 97% identical, or at least about 98% identical, or at least about 99% identical (or any percent identity between 45% and 99%, in whole integer increments), to the amino acid sequence of the reference protein. In one embodiment, the homologue comprises, consists essentially of, or consists of, an amino acid sequence that is less than 100% identical, less than about 99% identical, less than about 98% identical, less than about 97% identical, less than about 96% identical, less than about 95% identical; and so on, in increments of 1%, to less than about 70% identical to the naturally occurring amino acid sequence of the reference protein.

As used herein, unless otherwise specified, reference to a percent (%) identity refers to an evaluation of homology which is performed using: (1) a BLAST 2.0 Basic BLAST homology search using blastp for amino acid searches and blastn for nucleic acid searches with standard default parameters, wherein the query sequence is filtered for low complexity regions by default (described in Altschul, S. F., Madden, T. L., Schääffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.” Nucleic Acids Res. 25:3389-3402, incorporated herein by reference in its entirety); (2) a BLAST 2 alignment (using the parameters described below); (3) and/or PSI-BLAST with the standard default parameters (Position-Specific Iterated BLAST. It is noted that due to some differences in the standard parameters between BLAST 2.0 Basic BLAST and BLAST 2, two specific sequences might be recognized as having significant homology using the BLAST 2 program, whereas a search performed in BLAST 2.0 Basic BLAST using one of the sequences as the query sequence may not identify the second sequence in the top matches. In addition, PSI-BLAST provides an automated, easy-to-use version of a “profile” search, which is a sensitive way to look for sequence homologues. The program first performs a gapped BLAST database search. The PSI-BLAST program uses the information from any significant alignments returned to construct a position-specific score matrix, which replaces the query sequence for the next round of database searching. Therefore, it is to be understood that percent identity can be determined by using any one of these programs.

Two specific sequences can be aligned to one another using BLAST 2 sequence as described in Tatusova and Madden, (1999), “Blast 2 sequences—a new tool for comparing protein and nucleotide sequences”, FEMS Microbiol Lett. 174:247-250, incorporated herein by reference in its entirety. BLAST 2 sequence alignment is performed in blastp or blastn using the BLAST 2.0 algorithm to perform a Gapped BLAST search (BLAST 2.0) between the two sequences allowing for the introduction of gaps (deletions and insertions) in the resulting alignment. For purposes of clarity herein, a BLAST 2 sequence alignment is performed using the standard default parameters as follows.

For blastn, using 0 BLOSUM62 matrix:

Reward for match=1

Penalty for mismatch=−2

Open gap (5) and extension gap (2) penalties

gap x_dropoff (50) expect (10) word size (11) filter (on)

For blastp, using 0 BLOSUM62 matrix:

Open gap (11) and extension gap (1) penalties

gap x_dropoff (50) expect (10) word size (3) filter (on).

Also included in the present invention are antibodies and antigen binding fragments thereof that selectively bind to any of the proteins associated with angiogenesis described herein, as well as the use of such antibodies and antigen binding fragments thereof in any of the methods described herein. Antibodies that selectively bind to a protein can be produced using the structural information available for the protein (e.g., the amino acid sequence of at least a portion of the protein). More specifically, the phrase “selectively binds” refers to the specific binding of one protein to another (e.g., an antibody, fragment thereof, or binding partner to an antigen), wherein the level of binding, as measured by any standard assay (e.g., an immunoassay), is statistically significantly higher than the background control for the assay. For example, when performing an immunoassay, controls typically include a reaction well/tube that contain antibody or antigen binding fragment alone (i.e., in the absence of antigen), wherein an amount of reactivity (e.g., non-specific binding to the well) by the antibody or antigen binding fragment thereof in the absence of the antigen is considered to be background. Binding can be measured using a variety of methods standard in the art including enzyme immunoassays (e.g., ELISA), immunoblot assays, etc.). Antibodies useful in the assay kit and methods of the present invention can include polyclonal and monoclonal antibodies, divalent and monovalent antibodies, bi- or multi-specific antibodies, serum containing such antibodies, antibodies that have been purified to varying degrees, and any functional equivalents of whole antibodies. Isolated antibodies of the present invention can include serum containing such antibodies, or antibodies that have been purified to varying degrees. Whole antibodies of the present invention can be polyclonal or monoclonal. Alternatively, functional equivalents of whole antibodies, such as antigen binding fragments in which one or more antibody domains are truncated or absent (e.g., Fv, Fab, Fab′, or F(ab)₂ fragments), as well as genetically-engineered antibodies or antigen binding fragments thereof, including single chain antibodies or antibodies that can bind to more than one epitope (e.g., bi-specific antibodies), or antibodies that can bind to one or more different antigens (e.g., bi- or multi-specific antibodies), may also be employed in the invention.

Genetically engineered antibodies include those produced by standard recombinant DNA techniques involving the manipulation and re-expression of DNA encoding antibody variable and/or constant regions. Particular examples include, chimeric antibodies, where the V_(H) and/or V_(L) domains of the antibody come from a different source to the remainder of the antibody, and CDR grafted antibodies (and antigen binding fragments thereof), in which at least one CDR sequence and optionally at least one variable region framework amino acid is (are) derived from one source and the remaining portions of the variable and the constant regions (as appropriate) are derived from a different source. Construction of chimeric and CDR-grafted antibodies are described, for example, in European Patent Applications: EP-A 0194276, EP-A 0239400, EP-A 0451216 and EP-A 0460617.

Generally, in the production of an antibody, a suitable experimental animal, such as, for example, but not limited to, a rabbit, a sheep, a hamster, a guinea pig, a mouse, a rat, or a chicken, is exposed to an antigen against which an antibody is desired. Typically, an animal is immunized with an effective amount of antigen that is injected into the animal. An effective amount of antigen refers to an amount needed to induce antibody production by the animal. The animal's immune system is then allowed to respond over a pre-determined period of time. The immunization process can be repeated until the immune system is found to be producing antibodies to the antigen. In order to obtain polyclonal antibodies specific for the antigen, serum is collected from the animal that contains the desired antibodies (or in the case of a chicken, antibody can be collected from the eggs). Such serum is useful as a reagent. Polyclonal antibodies can be further purified from the serum (or eggs) by, for example, treating the serum with ammonium sulfate.

Monoclonal antibodies may be produced according to the methodology of Kohler and Milstein (Nature 256:495-497, 1975). For example, B lymphocytes are recovered from the spleen (or any suitable tissue) of an immunized animal and then fused with myeloma cells to obtain a population of hybridoma cells capable of continual growth in suitable culture medium. Hybridomas producing the desired antibody are selected by testing the ability of the antibody produced by the hybridoma to bind to the desired antigen.

The invention also extends to non-antibody polypeptides, sometimes referred to as antigen binding partners or antigen binding peptides, that have been designed to bind selectively to the protein of interest. Examples of the design of such polypeptides, which possess a prescribed ligand specificity are given in Beste et al. (Proc. Natl. Acad. Sci. 96:1898-1903, 1999), incorporated herein by reference in its entirety.

One embodiment of the present invention relates to a method to identify a compound useful for the inhibition (reduction, decrease) of angiogenesis, which may also be applied to identifying agents useful for inhibition of tumor cell growth, presence, or malignancy. A similar method of the present invention can also be used to identify a compound useful for the promotion (increase, initiation, enhancement) of angiogenesis, which may also be applied to identifying agents useful for conditions in which angiogenesis may be desired (e.g., stroke, ischemia).

Either of such methods generally includes the steps of: (a) detecting an initial level of the expression or activity of one or more genes or proteins encoded thereby (biomarkers) that are associated with angiogenesis as described herein (e.g., any one or more of the genes or the proteins encoded by a gene or nucleic acid sequence referenced in Table I, Table IV, Table V, and/or Table VI, and/or any one or more of the genes or proteins specifically described herein by reference to a particular nucleic acid or amino acid sequence) in a cell or soluble sample or product derived from the cell (e.g., cell supernate); (b) contacting the cell with a test compound; (c) detecting a level of gene or protein expression or activity in the cell (or sample derived therefrom) after contact of the cell with the compound; and, (d) selecting a compound that regulates the level of gene or protein expression or activity in the cell, as compared to prior to contact with the test compound. In one embodiment, the biomarker is a protein, or the gene encoding such protein, selected from: ADAMts7, CRELD-2, Decorin, ECM1, Inhibin β-b, Integrin α-3, Integrin α-6, Lipocalin-7, Loxl-3, Lumican, MAGP-2, Matrilin-2, Nephronectin, SerpinE2, and/or SMOC-2. These genes and proteins have been described in detail above.

In another embodiment, the biomarker is a gene, or the protein encoded by the gene, selected from: 0610007C21Rik, apoptosis related protein APR-3, 1810014L12Rik, Cd14 (encoding CD14 antigen represented herein by SEQ ID NO:5 and SEQ ID NO:6), Cd38 (comprising a nucleic acid sequence represented herein by SEQ ID NO:7 and encoding CD38 antigen); Cd53 (encoding CD53 antigen represented herein by SEQ ID NO:8 and SEQ ID NO:9), Emp2 (encoding epithelial membrane protein represented herein by SEQ ID NO:10 and SEQ ID NO:11), Fcgrt (encoding Fc receptor (IgG, alpha chain transporter) represented herein by SEQ ID NO:12 and SEQ ID NO:13), Islr (encoding immunoglobulin superfamily containing leucine-rich repeat represented herein by SEQ ID NO:14 and SEQ ID NO:15); Lrp2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:16 and SEQ ID NO:17 and encoding low density lipoprotein receptor-related protein 2); Ly6a (encoding lymphocyte antigen 6 complex, locus A represented herein by SEQ ID NO:18); P2rx4 (encoding purinergic receptor P2X, ligand-gated ion channel 4, represented herein by SEQ ID NO:19 and SEQ ID NO:20; Pcdhb9 (encoding protocadherin beta 9 represented herein by SEQ ID NO:21 and SEQ ID NO:22); Ptpre (encoding protein tyrosine phosphatase receptor type E represented herein by SEQ ID NO:23 and SEQ ID NO:24); Slc4a3 (encoding solute carrier family 4 (anion exchanger) member 3, represented herein by SEQ ID NO:25 and SEQ ID NO:26); and/or Tmc6 (encoding transmembrane channel-like gene family 6, represented herein by SEQ ID NO:27).

In yet another embodiment, the biomarker is a gene, or the protein encoded by the gene, selected from: 9130213B05Rik (encoding a protein represented herein by SEQ ID NO:29); C1s (encoding complement component 1, s subcomponent, represented herein by SEQ ID NO:34 and SEQ ID NO:35); C3 (encoding complement component 3 represented herein by SEQ ID NO:30 and SEQ ID NO:31); Cfh (comprising a nucleic acid sequence represented herein by SEQ ID NO:32 and SEQ ID NO:33 and encoding complement component factor h); Col9a3 (comprising a nucleic acid sequence represented herein by SEQ ID NO:36 and SEQ ID NO:37 and encoding procollagen, type IX, alpha 3); Grem1 (encoding cysteine knot superfamily 1, BMP antagonist 1, represented herein by SEQ ID NO:38 and SEQ ID NO:39); Loxl3 (encoding lysyl oxidase-like 3, represented herein by SEQ ID NO:40 and SEQ ID NO:41); MAGP-2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:123 and SEQ ID NO:124 and encoding microfibril-associated glycoprotein-2, represented herein by SEQ ID NO:42 and SEQ ID NO:43); Mglap (encoding matrix gamma-carboxyglutamate (gla) protein represented herein by SEQ ID NO:44 and SEQ ID NO:45); Naga (encoding N-acetyl galactosaminidase, alpha, represented herein by SEQ ID NO:46 and SEQ ID NO:47); Nbl1 (encoding neuroblastoma, suppression of tumorigenicity 1, represented herein by SEQ ID NO:48 and SEQ ID NO:49); Ngfb (encoding nerve growth factor, beta, represented herein by SEQ ID NO:50 and SEQ ID NO:51), Npnt (represented herein by SEQ ID NO:52 and SEQ ID NO:53 and encoding nephronectin); Olfm1 (encoding olfactomedin 1, represented herein by SEQ ID NO:54 and SEQ ID NO:55); and/or U90926 (encoding a protein represented herein by SEQ ID NO:56).

In yet another embodiment, the biomarker is a gene, or the protein encoded by the gene, selected from any of the genes or proteins specifically identified by a sequence described herein.

Typically, compounds that regulate the expression or activity of the gene or protein in the presence of the compound in the manner that has been associated by the present inventors with angiogenesis can be selected as pro-angiogenic agents or anti-angiogenesis targets (agents that are targets for inhibition in order to inhibit angiogenesis), and compounds that regulate the expression or activity of the gene or protein in the presence of the compound in a manner that is opposite or contrary to the manner that has been associated by the present inventors with angiogenesis, can be selected as anti-angiogenic agents. The method can include a further step of detecting whether a compound selected in (d) has or regulates pro-angiogenic activity or anti-angiogenic activity, such as in a bioassay for angiogenesis described herein.

Detection of the regulation of the expression of a gene (or the protein encoded thereby) in the “manner” associated with the established level of expression for that gene during angiogenesis, at a minimum, refers to the detection of the regulation of a gene that has now been shown by the present inventors to be selectively regulated in during angiogenesis, in the same direction (i.e., upregulation or downregulation) and at a similar or comparable level, as compared to a normal control (the level of expression of the gene that has been or is established under normal, or non-angiogenic conditions). In other words, if “gene X” is upregulated during angiogenesis as compared to a normal control level of expression, then one determines whether the expression of gene X is upregulated in as compared to a normal control, or whether the expression of gene X is more similar to the level of expression of the normal control. In one aspect of the invention, a gene identified as being upregulated or downregulated as compared to a baseline control according to the invention is regulated in the same direction and to at least about 10%, and more preferably at least 20%, and more preferably at least 25%, and more preferably at least 30%, and more preferably at least 35%, and more preferably at least 40%, and more preferably at least 45%, and more preferably at least 50%, and preferably at least 55%, and more preferably at least 60%, and more preferably at least 65%, and more preferably at least 70%, and more preferably at least 75%, and more preferably at least 80%, and more preferably at least 85%, and more preferably at least 90%, and more preferably at least 95%, or even higher (e.g., above 100%) of the level of expression of the gene that has been established during angiogenesis. Statistical significance should be at least p<0.05, and more preferably, at least p<0.01, and more preferably, p<0.005, and even more preferably, p<0.001.

Steps (a) and (c) of the method of the present invention require detection of the biomarker (gene or protein encoded thereby) expression and/or biological activity in a cell or in a sample derived from the cell, such as a cellular extract or supernate. Detection of biomarker expression and/or biological activity can include, but is not limited to: detecting biomarker mRNA transcription (e.g., by polymerase chain reaction (PCR), reverse transcriptase-PCR (RT-PCR), in situ hybridization, Northern blot, sequence analysis or detection of a reporter gene); detecting biomarker translation (e.g., by immunoblot, enzyme-linked immunosorbant assay (ELISA), radioimmunoassay (RIA), immunoprecipitation, immunohistochemistry and immunofluorescence); and/or detecting biomarker biological activity (e.g., by detecting any of the activities of the particular biomarker, such as enzyme activity, receptor binding, induction of a growth factor, a cell signal transduction event, etc.). The step of detection in step (a) is the control level of biomarker expression or biological activity for a cell to which the detection in step (c) is to be compared and evaluated. The step of detection in step (c) is the experimental level of biomarker expression or biological activity which indicates whether the test compound can change the level of biomarker expression or biological activity in the cell, as compared to the level determined in step (a). In other words, the assay determines whether a given compound is capable of regulating the expression or activity of the biomarker (up or down), and therefore can predicted to regulate angiogenesis.

One can use a tumor cell or a normal, non-tumor cell, such as an endothelial cell, or a sample derived therefrom, in this assay, in order to identify compounds that regulate biomarker-associated angiogenesis, including angiogenesis that is associated with tumor cells, or to identify compounds in order to screen for putative carcinogens.

A cell suitable for use in the present method is any cell which expresses or can be induced to express, a detectable level of the biomarker of interest. A detectable level of biomarker is a level which can be detected using any of the methods for biomarker detection described herein. Since the biomarkers identified herein are expressed by many mammalian cell types, a variety of cell types could be selected. However, it will be appreciated by those of skill in the art that some cell types are more suitable for use in an in vitro assay (e.g., easy to maintain in culture, easy to obtain), and that certain biomarkers may be more readily detectable in some cell types, and therefore, such cell types are preferable for use in the present invention. A preferred cell type to use in the method of the present invention is any cell type that has a high expression or low expression of the biomarker in a tumor cell as compared to a non-tumor cell of the same cell type, or has a high expression or low expression of the biomarker under angiogenic conditions as compared to non-angiogenic conditions, so that a change in biomarker expression or activity is readily detectable. As discussed above, one can also use a sample derived from such a cell, such as a cell extract or cell supemate. Some preferred cells to use in the method of the present invention include, but are not limited to: fibroblasts (and fibrosarcomas), epithelial cells, endothelial cells, and breast, colon, kidney, ovarian or uterine tumor cells and non-tumor cells that endogenously or recombinantly express the biomarker. In one embodiment, a cell suitable for use in any aspect the general assay method is a cell which has been transfected with a recombinant nucleic acid molecule encoding the biomarker and operatively linked to a transcription control sequence so that the biomarker is expressed by the cell. Methods and reagents for preparing recombinant cells are known in the art.

As used herein, the term “putative regulatory compound” refers to compounds having an unknown or previously unappreciated regulatory activity in a particular process. The above-described method for identifying a compound of the present invention includes a step of contacting a test cell with a compound being tested for its ability to regulate the expression or biological activity of the biomarker. For example, test cells can be grown in liquid culture medium or grown on solid medium in which the liquid medium or the solid medium contains the compound to be tested. In addition, as described above, the liquid or solid medium contains components necessary for cell growth, such as assimilable carbon, nitrogen and micronutrients.

The above-described methods, in one aspect, involve contacting cells with the compound being tested for a sufficient time to allow for interaction of the putative regulatory compound with an element that affects biomarker expression and/or biological activity in a cell. Such elements can include, but are not limited to: a nucleic acid molecule encoding the biomarker (including regulatory regions of such a molecule), the biomarker protein, biomarker inhibitors, biomarker stimulators, and biomarker substrates. The period of contact with the compound being tested can be varied depending on the result being measured, and can be determined by one of skill in the art. For example, for binding assays, a shorter time of contact with the compound being tested is typically suitable, than when activity or expression is assessed. As used herein, the term “contact period” refers to the time period during which cells are in contact with the compound being tested. The term “incubation period” refers to the entire time during which cells are allowed to grow prior to evaluation, and can be inclusive of the contact period. Thus, the incubation period includes all of the contact period and may include a further time period during which the compound being tested is not present but during which growth is continuing (in the case of a cell based assay) prior to scoring. The incubation time for growth of cells can vary but is sufficient to allow for the upregulation or downregulation of biomarker expression or biological activity in a cell. It will be recognized that shorter incubation times are preferable because compounds can be more rapidly screened. A preferred incubation time is between about 1 hour to about 48 hours.

The conditions under which the cell or cell lysate of the present invention is contacted with a putative regulatory compound, such as by mixing, are any suitable culture or assay conditions and includes an effective medium in which the cell can be cultured or in which the cell lysate can be evaluated in the presence and absence of a putative regulatory compound. Cells of the present invention can be cultured in a variety of containers including, but not limited to, tissue culture flasks, test tubes, microtiter dishes, and petri plates. Culturing is carried out at a temperature, pH and carbon dioxide content appropriate for the cell. Such culturing conditions are also within the skill in the art. Cells are contacted with a putative regulatory compound under conditions which take into account the number of cells per container contacted, the concentration of putative regulatory compound(s) administered to a cell, the incubation time of the putative regulatory compound with the cell, and the concentration of compound administered to a cell. Determination of effective protocols can be accomplished by those skilled in the art based on variables such as the size of the container, the volume of liquid in the container, conditions known to be suitable for the culture of the particular cell type used in the assay, and the chemical composition of the putative regulatory compound (i.e., size, charge etc.) being tested. A preferred amount of putative regulatory compound(s) comprises between about 1 nM to about 10 mM of putative regulatory compound(s) per well of a 96-well plate.

In one aspect, the present method also makes use of non-cell based assay systems to identify compounds that can regulate biomarker expression or biological activity and thereby are predicted to be useful for regulating cell growth. For example, biomarker proteins and nucleic acid molecules encoding the biomarker may be recombinantly expressed and utilized in non-cell based assays to identify compounds that bind to the protein or nucleic acid molecule, respectively. In non-cell based assays the recombinantly expressed biomarker or nucleic acid encoding the biomarker is attached to a solid substrate such as a test tube, microtiter well or a column, by means well known to those in the art.

In one embodiment, DNA encoding a reporter molecule can be linked to a regulatory element of the biomarker gene (or a gene encoding a protein that directly regulates the biomarker) and used in appropriate intact cells, cell extracts or lysates to identify compounds that modulate biomarker gene expression, respectively. Appropriate cells or cell extracts are prepared from any cell type that normally expresses the biomarker, thereby ensuring that the cell extracts contain the transcription factors required for in vitro or in vivo transcription. The screen can be used to identify compounds that modulate the expression of the reporter construct. In such screens, the level of reporter gene expression is determined in the presence of the test compound and compared to the level of expression in the absence of the test compound.

Following steps (a), (b) and (c) of the method to identify a compound that regulates the biomarker is a step (d) of selecting a compound that regulates (up or down) the level of the biomarker expression or activity in the cell, as compared to in the absence of the compound. Compounds which cause a regulation (increase or decrease) in the level of biomarker expression or biological activity are selected by the present method as being compounds that are predicted to be useful as pro-angiogenesis agents or anti-angiogenesis agents (or targets for regulation of angiogenesis), depending on how the biomarker has been correlated with angiogenesis according to the description provided herein.

Preferably, compounds which are selected in step (d) are compounds for which, after the test cell was contacted with the compound in step (b), the level of biomarker expression or biological activity detected in step (c) was statistically significantly changed (i.e., with at least a 95% confidence level, or p<0.05) as compared to the initial level of biomarker expression or biological activity detected in step (a). Preferably, detection of at least about a 30% change in biomarker expression or biological activity in the cell as compared to initial level results in selection of the compound according to step (d). More preferably, detection of at least about a 50% change and more preferably at least about a 70% change, and more preferably at least about a 90% change, or any percentage change between 5% and higher in 1% increments (i.e., 5%, 6%, 7%, 8% . . . ) in biomarker expression or biological activity in the cell as compared to the initial level results in selection of the compound according to step (d). In one embodiment, a 1.5 fold change in biomarker expression or biological activity in the cell as compared to the initial level results in selection of the compound according to step (d). More preferably, detection of at least about a 3 fold change, and more preferably at least about a 6 fold change, and even more preferably, at least about a 12 fold change, and even more preferably, at least about a 24 fold change, or any fold change from 1.5 up in increments of 0.5 fold (i.e., 1.5, 2.0, 2.5, 3.0 . . . ) in biomarker expression or biological activity as compared to the initial level, results in selection of the compound according to step (d).

It is to be understood that either of steps (a) and (c) of detection in any of the methods to identify a compound described above can result in no detection, or no change in detection, of biomarker expression or biological activity. In addition, since the level of biomarker expression or biological activity in step (a) (i.e., the initial level) is one of the control levels of biomarker for the assay (i.e., in the absence of the test compound), if step (a) reveals no detectable biomarker expression or biological activity, then any detectable level of biomarker expression or biological activity in step (c) is considered to be a positive result and indicative of increased biomarker activity in the cell and the appropriate assessment associated with this result. If the initial level of biomarker expression or biological activity in step (a) is a detectable level, then the level of biomarker expression or biological activity detected in step (c) is evaluated to determine whether it is statistically significantly greater than or less than that of step (a). It is possible that the level of biomarker expression or biological activity in step (c) could be no detectable change, which would indicate that the compound did not increase or decrease biomarker activity. In this scenario, however, it should be determined that the test cell can display an increase or decrease in the particular biomarker expression or biological activity under some conditions (i.e., by contact with a compound known to increase the biomarker activity in the test cell), so that false negatives are not identified.

In one embodiment of this method to identify regulators of biomarkers of the present invention, the method further includes the step of detecting whether the compound selected in step (d) can inhibit tumor cell formation or a characteristic thereof. In this embodiment, the test cell is contacted with the compound as in step (b), and the growth characteristics of the cell before and after contact with the cell are evaluated. Evaluation of cell growth can be by any suitable method in the art, including, but not limited to, proliferation assays (e.g., by measuring uptake of [³H]-thymidine, viewing cells morphologically) and/or evaluating markers of cell growth (e.g., measurement of changes in cell surface markers, measurement of intracellular indicators of cell growth). Such methods are known in the art and are exemplified in the attached examples.

Compounds suitable for testing and use in the methods of the present invention include any known or available proteins, nucleic acid molecules, as well as products of drug design, including peptides, oligonucleotides, carbohydrates and/or synthetic organic molecules. Such an agent can be obtained, for example, from molecular diversity strategies (a combination of related strategies allowing the rapid construction of large, chemically diverse molecule libraries), libraries of natural or synthetic compounds, in particular from chemical or combinatorial libraries (i.e., libraries of compounds that differ in sequence or size but that have the same building blocks) or by rational drug design. See for example, Maulik et al., 1997, supra. Candidate compounds initially identified by drug design methods can be screened for the ability to modulate the expression and/or biological activity of the biomarker using the methods described herein.

Compounds identified by the method described above can be used in a method to regulate angiogenesis, treat a condition or reduce a symptom of a condition in which inhibition of angiogenesis is desirable (e.g.,cancer), or treat a condition or reduce a symptom of a condition in which promotion of angiogenesis is desirable (e.g.,ischemia, stroke), as described herein and any such compounds are encompassed for use in the method described below.

More particularly, according to one embodiment of the present invention, administration of a compound or composition of the invention or targeting of a biomarker of the invention is useful to inhibit the tumorigenicity of a target cell or to inhibit angiogenesis in a tissue of a patient. Typically, it is desirable to inhibit the growth of a target cell (e.g., a tumor) to obtain a therapeutic benefit in the patient. In one embodiment, patients whom are suitable candidates for methods of the present invention include, but are not limited to, patients that have, or are at risk of developing (e.g., are predisposed to), cancer or a lymphoproliferative disease, or any condition in which regulation of angiogenesis might be beneficial. Particular conditions that are characterized or caused by abnormal or excessive angiogenesis, and therefore may be treated using the methods and compositions of the invention include, but are not limited to: cancer (e.g., activation of oncogenes, loss of tumor suppressors); infectious diseases (e.g., pathogens express angiogenic genes, enhance angiogenic programs); autoimmune disorders (e.g., activation of mast cells and other leukocytes); vascular malformations (e.g., Tie-2 mutation); DiGeorge syndrome (e.g., low VEGF and neuropilin-1 expression); HHT (e.g., mutations of endoglin or LK-1), cavernous hemangioma (e.g., loss of Cx37 and Cx40); atherosclerosis; transplant ateriopathy; obesity (e.g., angiogenesis induced by fatty diet, weight loss by angiogenesis inhibitors); psoriasis; warts; allergic dermatitis; scar keloids; pyogenic granulomas; blistering disease; Kaposi sarcoma in AIDS patients; persistent hyperplastic vitreous syndrome (e.g., loss of Ang-2 or VEGF164); diabetic retinopathy; retinopathy of prematurity; choroidal neovascularization (e.g., TIMP-3 mutation); primary pulmonary hypertension (e.g., germline BMPR-2 mutation, somatic EC mutation); asthma; nasal polyps; inflammatory bowel disease; periodontal disease; ascites; peritoneal adhesions; endometriosis; uterine bleeding; ovarian cysts; ovarian hyperstimulation; arthritis; synovitis; osteomyelitis; and osteophyte formation.

In another embodiment of the invention, administration of a compound or composition of the invention or targeting of a biomarker of the invention is useful to promote angiogenesis. Patients whom are suitable candidates for such a method of the invention include, but are not limited to: patients with vascular deficiencies, cardiovascular disease, or patients in whom stimulation of endothelial cell activation and stabilization of newly formed microvessels or other vessels would be beneficial. For example, such conditions include, but are not limited to, stroke, ischemia and related conditions.

Therefore, yet another embodiment of the invention relates to methods to increase or decrease the expression or biological activity of any one or more of the biomarkers described herein (e.g., Table I, Table IV, Table V, and/or Table VI) in cells (e.g., isolated cells, cells of a tissue, cells in a patient) in order to achieve a goal. This goal can include, but is not limited to, reduction of angiogenesis in a tissue, decreased tumorigenicity of tumor cells, or reduction in the potential for development of tumor cells, enhancement or promotion of angiogenesis in a tissue, or treatment of a disease or condition in which enhanced angiogenesis would be desirable. Such methods generally include the step of increasing or decreasing the expression and/or biological activity of one or more biomarkers described herein, as required for a given cell type, in order to achieve the desired result (e.g., inhibition or promotion of angiogenesis, cancer inhibition, etc.). In one embodiment, the biomarker is a protein, or the gene encoding such protein, selected from: ADAMts7, CRELD-2, Decorin, ECM1, Inhibin β-b, Integrin α-3, Integrin α-6, Lipocalin-7, Loxl-3, Lumican, MAGP-2, Matrilin-2, Nephronectin, SerpinE2, and/or SMOC-2.

In another embodiment, the biomarker is a gene, or the protein encoded by the gene, selected from: 0610007C21Rik, apoptosis related protein APR-3, 1810014L12Rik, Cd14 (encoding CD14 antigen represented herein by SEQ ID NO:5 and SEQ ID NO:6), Cd38 (comprising a nucleic acid sequence represented herein by SEQ ID NO:7 and encoding CD38 antigen); Cd53 (encoding CD53 antigen represented herein by SEQ ID NO:8 and SEQ ID NO:9), Emp2 (encoding epithelial membrane protein represented herein by SEQ ID NO:10 and SEQ ID NO:11), Fcgrt (encoding Fc receptor (IgG, alpha chain transporter) represented herein by SEQ ID NO:12 and SEQ ID NO:13), Islr (encoding immunoglobulin superfamily containing leucine-rich repeat represented herein by SEQ ID NO:14 and SEQ ID NO:15); Lrp2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:16 and SEQ ID NO:17 and encoding low density lipoprotein receptor-related protein 2); Ly6a (encoding lymphocyte antigen 6 complex, locus A represented herein by SEQ ID NO:18); P2rx4 (encoding purinergic receptor P2X, ligand-gated ion channel 4, represented herein by SEQ ID NO:19 and SEQ ID NO:20; Pcdhb9 (encoding protocadherin beta 9 represented herein by SEQ ID NO:21 and SEQ ID NO:22); Ptpre (encoding protein tyrosine phosphatase receptor type E represented herein by SEQ ID NO:23 and SEQ ID NO:24); Slc4a3 (encoding solute carrier family 4 (anion exchanger) member 3, represented herein by SEQ ID NO:25 and SEQ ID NO:26); and/or Tmc6 (encoding transmembrane channel-like gene family 6, represented herein by SEQ ID NO:27).

In yet another embodiment, the biomarker is a gene, or the protein encoded by the gene, selected from: 9130213B05Rik (encoding a protein represented herein by SEQ ID NO:29); C1s (encoding complement component 1, s subcomponent, represented herein by SEQ ID NO:34 and SEQ ID NO:35); C3 (encoding complement component 3 represented herein by SEQ ID NO:30 and SEQ ID NO:31); Cfh (comprising a nucleic acid sequence represented herein by SEQ ID NO:32 and SEQ ID NO:33 and encoding complement component factor h); Col9a3 (comprising a nucleic acid sequence represented herein by SEQ ID NO:36 and SEQ ID NO:37 and encoding procollagen, type IX, alpha 3); Grem1 (encoding cysteine knot superfamily 1, BMP antagonist 1, represented herein by SEQ ID NO:38 and SEQ ID NO:39); Loxl3 (encoding lysyl oxidase-like 3, represented herein by SEQ ID NO:40 and SEQ ID NO:41); MAGP-2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:123 and SEQ ID NO:124 and encoding microfibrillar associated protein 5, represented herein by SEQ ID NO:42 and SEQ ID NO:43); Mglap (encoding matrix gamma-carboxyglutamate (gla) protein represented herein by SEQ ID NO:44 and SEQ ID NO:45); Naga (encoding N-acetyl galactosaminidase, alpha, represented herein by SEQ ID NO:46 and SEQ ID NO:47); Nbl1 (encoding neuroblastoma, suppression of tumorigenicity 1, represented herein by SEQ ID NO:48 and SEQ ID NO:49); Ngfb (encoding nerve growth factor, beta, represented herein by SEQ ID NO:50 and SEQ ID NO:51), Npnt (represented herein by SEQ ID NO:52 and SEQ ID NO:53 and encoding nephronectin); Olfm1 (encoding olfactomedin 1, represented herein by SEQ ID NO:54 and SEQ ID NO:55); and/or U90926 (encoding a protein represented herein by SEQ ID NO:56).

In yet another embodiment, the biomarker is a gene, or the protein encoded by the gene, selected from any of the genes or proteins specifically identified by a sequence described herein.

In the method of the present invention wherein the goals are to reduce angiogenesis in a tissue, decrease tumorigenicity of tumor cells, decrease tumor burden, increase survival, or reduce the potential for the development of tumor cells, preferably, cells that are targeted by the method are cells which, prior to the application of the present method, are exhibiting inappropriate (malignant) cell growth or a potential therefore, or cells in a tissue where it is desirable to inhibit angiogenesis. Preferred cells to regulate according to this aspect of the present invention include tumor cells. Cells in which it is desirable to inhibit tumorigenicity or tissues in which inhibition of angiogenesis is desired can be identified, for example, using the method for assessing the presence of cancer cells or biomarker expression and activity of the present invention as described in detail above. Such methods are particularly useful in patients where increased tumorigenicity (or simply tumor growth) or angiogenesis is, or is predicted to become, problematic. Therefore, such a method is particularly useful to treat patients that have, or are at a risk of developing, tumor cells (i.e., a cancer), or to treat any other patients having a condition characterized by undesirable cell growth (e.g., lymphoproliferative disorders). Other diseases and conditions in which inhibition of tumorigenicity or angiogenesis would be desirable will be apparent to those of skill in the art (many are discussed below) and are intended to be encompassed by the present invention.

Similarly, in the method of the present invention wherein the goals are to enhance or promote angiogenesis in a tissue, preferably, cells that are targeted by the method are cells in a tissue where it is desirable to promote angiogenesis. Preferred cells to regulate according to this aspect of the present invention include vascular endothelial cells. Such methods are particularly useful in patients where increased angiogenesis may be useful, such as in patients that have a vascular insufficiency or where the promotion of vascular stabilization and development is desired. Therefore, such a method is particularly useful to treat patients with vascular deficiencies, cardiovascular disease, or to stimulate endothelial cell activation and stabilization of newly formed microvessels or other vessels. Conditions in which promotion of angiogenesis would be desirable will be apparent to those of skill in the art and are intended to be encompassed by the present invention.

Accordingly, the method of the present invention includes a step of modulating (i.e., upregulating or downregulating) biomarker expression and/or biological activity in a patient that has, or is at risk of developing, inappropriate or unregulated cell growth (e.g., tumors) or angiogenesis, or a patient or subject that is in need of promotion of angiogenesis, depending on the goal of the therapy, as discussed above. Modulating biomarker expression or biological activity according to the present invention can be accomplished by directly affecting biomarker expression (transcription or translation) or biological activity, or by directly affecting the ability of a regulator (inhibitor or stimulator) of the biomarker to bind to the biomarker or to activate the biomarker. Preferably, the method of the present invention is targeted to a particular type of cell or tissue or region of the body in which inhibition of cell growth or regulation of angiogenesis is desired. A targeted cell, for example, could include a tumor cell, wherein the method does not substantially affect biomarker expression or biological activity in non-tumor cells, or in cells of a different type that the tumor cell type. Therefore, the method of the present invention, in one embodiment, is intended to be specifically targeted to biomarker expression and/or biological activity for the purpose of inhibiting or promoting cell growth, or inhibiting or promoting angiogenesis by modulating biomarker expression and/or biological activity.

An increase in biomarker expression and/or biological activity is defined herein as any measurable (detectable) increase (i.e., upregulation, stimulation, enhancement) of the expression or activity of the biomarker. As used herein, to increase biomarker expression and/or biological activity refers to any measurable increase in biomarker expression and/or biological activity by any suitable method of measurement. A decrease in biomarker expression and/or biological activity is defined herein as any measurable (detectable) decrease (i.e., downregulation, inhibition, reduction) of the expression or activity of biomarker. As used herein, to decrease biomarker expression and/or biological activity refers to any measurable decrease in the biomarker expression and/or biological activity by any suitable method of measurement.

Accordingly, one embodiment of the present invention includes the use of a variety of agents (i.e., regulatory compounds) which, by acting directly on the biomarker (or by being the biomarker gene encoding a protein or the biomarker protein itself) or by acting on inhibitors or stimulators of the biomarker or being an inhibitor or stimulator of the biomarker, modulate (regulate up or down) the expression and/or biological activity of the biomarker in a cell to produce a desired effect (e.g., inhibition of tumorigenesis or reduction of tumor burden or tumor stasis/increase of survival, inhibition or promotion of angiogenesis). Agents useful in the present invention include, for example, proteins, nucleic acid molecules, antibodies, and compounds that are products of rational drug design (i.e., drugs). Such compounds can be identified using the method of identifying compounds for regulating tumor cell growth and malignancy or for regulating angiogenesis as described above. Moreover, the expression or biological activity of the biomarker in a cell can be determined using the methods described above.

Therefore, in one embodiment, the method of the present invention increases the transcription and/or the translation of the biomarker by a cell that naturally expresses the biomarker and that is the target for growth regulation, or increases (stimulates, enhances) the biological activity of the biomarker. Methods for increasing the expression of a given biomarker include, but are not limited to, administering an agent that increases the expression or biological activity of the endogenous biomarker, administering biomarker protein or a homologue or analog (agonist) thereof to a subject, and/or overexpressing biomarker in target cells. In one aspect of this embodiment, the biomarker can be effectively overexpressed in a cell by increasing the activity of a promoter for the biomarker gene in the cell such that expression of endogenous biomarker in the cell is increased. For example, the activity of the biomarker gene promoter can be increased by methods which include, contacting the promoter with a transcriptional activator, inhibiting a biomarker promoter inhibitor, and increasing the activity of a biomarker promoter stimulator. Methods by which such compounds (e.g., transcriptional activators) can be administered to a cell are described below. In another embodiment, biomarker activity is increased by administering the biomarker or a homologue or analog (synthetic homologue or mimetic or compound) to the target cells or to the patient in an appropriate carrier or delivery vehicle.

In another embodiment, the method of the present invention decreases the transcription and/or the translation of the biomarker by a cell that naturally expresses the biomarker and that is the target for growth regulation, or inhibits the biological activity of biomarker. In this embodiment, it is desired to modify a target cell in order to decrease in biomarker gene expression, decrease the function of the gene, or decrease the function of the gene product (i.e., the protein encoded by the gene). Such methods can be referred to as inactivation (complete or partial), deletion, interruption, blockage or down-regulation of a gene encoding the biomarker. In one embodiment, reduction in biomarker activity or expression is achieved by use of a biomarker antagonist, antagonists having been described above.

In one aspect of this embodiment of the present invention, the expression and/or biological activity of the biomarker is increased by overexpressing the biomarker in the cell in which angiogenesis is to be regulated. Overexpression of a biomarker refers to an increase in expression of the biomarker over a normal, endogenous level of biomarker expression. For some cell types, which do not express detectable levels of the biomarker under normal conditions, such expression can be any detectable level. For cell types which do express detectable levels of the biomarker under normal conditions, an overexpression is any statistically significant increase in expression of the biomarker (p<0.05) (or constitutive expression where expression is normally not constitutive) over endogenous levels of expression. One method by which biomarker overexpression can be achieved is by transfecting the cell with a recombinant nucleic acid molecule encoding the biomarker operatively linked to a transcription control sequence, wherein the recombinant biomarker is expressed by the cell. As discussed previously herein, the nucleic acid sequence encoding biomarker, vectors suitable for expressing such a molecule, and methods of transfection of a cell with such a molecule, including in vivo methods, are known and are described in detail below.

A recombinant nucleic acid molecule expressing the biomarker is a molecule that can include at least one of any nucleic acid sequence encoding a protein having the biomarker biological activity operatively linked to at least one of any transcription control sequence capable of effectively regulating expression of the nucleic acid molecule(s) in the cell to be transfected. Although the phrase “nucleic acid molecule” primarily refers to the physical nucleic acid molecule and the phrase “nucleic acid sequence” primarily refers to the sequence of nucleotides on the nucleic acid molecule, the two phrases can be used interchangeably, especially with respect to a nucleic acid molecule, or a nucleic acid sequence, being capable of encoding a protein. In addition, the phrase “recombinant molecule” primarily refers to a nucleic acid molecule operatively linked to a transcription control sequence, but can be used interchangeably with the phrase “nucleic acid molecule” which is administered to an animal.

Preferably, a recombinant nucleic acid molecule is produced using recombinant DNA technology (e.g., polymerase chain reaction (PCR) amplification, cloning). Suitable nucleic acid sequences encoding the biomarker for use in a recombinant nucleic acid molecule of the present invention include any nucleic acid sequence that encodes the biomarker protein having biological activity and suitable for use in the target host cell. For example, when the target host cell is a human cell, human biomarker-encoding nucleic acid sequences are preferably used, although the present invention is not limited to strict use of naturally occurring sequences or same-species sequences.

A recombinant nucleic acid molecule includes a recombinant vector, which is any nucleic acid sequence, typically a heterologous sequence, which is operatively linked to the isolated nucleic acid molecule encoding a biomarker protein, which is capable of enabling recombinant production of the biomarker protein, and which is capable of delivering the nucleic acid molecule into a host cell according to the present invention. Such a vector can contain nucleic acid sequences that are not naturally found adjacent to the isolated nucleic acid molecules to be inserted into the vector. The vector can be either RNA or DNA, either prokaryotic or eukaryotic, and preferably in the present invention, is a virus or a plasmid. Recombinant vectors can be used in the cloning, sequencing, and/or otherwise manipulating of nucleic acid molecules. Recombinant vectors are preferably used in the expression of nucleic acid molecules, and can also be referred to as expression vectors. Preferred recombinant vectors are capable of being expressed in a transfected host cell, and particularly, in a transfected mammalian host cell in vivo.

In a recombinant molecule of the present invention, nucleic acid molecules are operatively linked to expression vectors containing regulatory sequences such as transcription control sequences, translation control sequences, origins of replication, and other regulatory sequences that are compatible with the host cell and that control the expression of nucleic acid molecules of the present invention. In particular, recombinant molecules of the present invention include nucleic acid molecules that are operatively linked to one or more transcription control sequences. The phrase “operatively linked” refers to linking a nucleic acid molecule to a transcription control sequence in a manner such that the molecule is expressed when transfected (i.e., transformed, transduced or transfected) into a host cell.

Transcription control sequences are sequences that control the initiation, elongation, and termination of transcription. Particularly important transcription control sequences are those that control transcription initiation, such as promoter, enhancer, operator and repressor sequences. Suitable transcription control sequences include any transcription control sequence that can function in a host cell according to the present invention. A variety of suitable transcription control sequences are known to those skilled in the art. Preferred transcription control sequences include those which function in mammalian cells, with cell- or tissue-specific transcription control sequences being particularly preferred. Examples of preferred transcription control sequences include, but are not limited to, transcription control sequences useful for expression of a protein in epithelial cells and tumor cells and the naturally occurring biomarker promoter. Particularly preferred transcription control sequences include inducible promoters, cell-specific promoters, tissue-specific promoters (e.g., insulin promoters) and enhancers. Suitable promoters for these and other cell types will be easily determined by those of skill in the art. Transcription control sequences of the present invention can also include naturally occurring transcription control sequences naturally associated with the protein to be expressed prior to isolation. In one embodiment, a transcription control sequence includes an inducible promoter.

One type of recombinant vector useful in a recombinant nucleic acid molecule of the present invention is a recombinant viral vector. Such a vector includes a recombinant nucleic acid sequence encoding a biomarker protein of the present invention that is packaged in a viral coat that can be expressed in a host cell in an animal or ex vivo after administration. A number of recombinant viral vectors can be used, including, but not limited to, those based on alphaviruses, poxviruses, adenoviruses, herpesviruses, lentiviruses, adeno-associated viruses and retroviruses. Particularly preferred viral vectors are those based on adenoviruses and adeno-associated viruses. Viral vectors suitable for gene delivery are well known in the art and can be selected by the skilled artisan for use in the present invention. A detailed discussion of current viral vectors is provided in “Molecular Biotechnology,” Second Edition, by Glick and Pasternak, ASM Press, Washington D.C., 1998, pp. 555-590, the entirety of which is incorporated herein by reference.

For example, a retroviral vector, which is useful when it is desired to have a nucleic acid sequence inserted into the host genome for long term expression, can be packaged in the envelope protein of another virus so that it has the binding specificity and infection spectrum that are determined by the envelope protein (e.g., a pseudotyped virus). In addition, the envelope gene can be genetically engineered to include a DNA element that encodes and amino acid sequence that binds to a cell receptor to create a recombinant retrovirus that infects a specific cell type. Expression of the biomarker gene can be further controlled by the use of a cell or tissue-specific promoter. Retroviral vectors have been successfully used to transfect cells with a gene which is expressed and maintained in a variety of ex vivo systems

An adenoviral vector is a preferred vector for use in the present method. An adenoviral vector infects a wide range of human cells and has been used extensively in live vaccines. Adenoviral vectors used in gene therapy do not integrate into the host genome, and therefore, gene therapy using this system requires periodic administration, although methods have been described which extend the expression time of adenoviral transferred genes, such as administration of antibodies directed against T cell receptors at the site of expression (Sawchuk et al., 1996, Hum. Gene. Ther. 7:499-506). The efficiency of adenovirus-mediated gene delivery can be enhanced by developing a virus that preferentially infects a particular target cell. For example, a gene for the attachment fibers of adenovirus can be engineered to include a DNA element that encodes a protein domain that binds to a cell-specific receptor. Examples of successful in vivo delivery of genes has been demonstrated and is discussed in more detail below.

Yet another type of viral vector is based on adeno-associated viruses, which are small, nonpathogenic, single-stranded human viruses. This virus can integrate into a specific site on chromosome 19. This virus can carry a cloned insert of about 4.5 kb, and has typically been successfully used to express proteins in vivo from 70 days to at least 5 months. Demonstrating that the art is quickly advancing in the area of gene therapy, however, a publication by Bennett et al. reported efficient and stable transgene expression by adeno-associated viral vector transfer in vivo for greater than 1 year (Bennett et al., 1999, Proc. Natl. Acad. Sci. USA 96:9920-9925).

Another type of viral vector that is suitable for use in the present invention is a herpes simplex virus vector. Herpes simplex virus type 1 infects and persists within nondividing neuronal cells, and is therefore a suitable vector for targeting and transfecting cells of the central and peripheral nervous system with a biomarker protein of the present invention. Preclinical trials in experimental animal models with such a vector has demonstrated that the vector can deliver genes to cells of both the brain and peripheral nervous system that are expressed and maintained for long periods of time.

Suitable host cells to transfect with a recombinant nucleic acid molecule according to the present invention include any mammalian cell that can be transfected. Host cells can be either untransfected cells or cells that are already transfected with at least one nucleic acid molecule. Host cells according to the present invention can be any cell capable of producing a biomarker protein as described herein or in which it is desired to produce the biomarker.

According to the present invention, a host cell can also be referred to as a target cell or a targeted cell in vivo, in which a recombinant nucleic acid molecule encoding a biomarker protein having the biological activity of the biomarker is to be expressed. As used herein, the term “target cell” or “targeted cell” refers to a cell to which a recombinant nucleic acid molecule of the present invention is selectively designed to be delivered. The term target cell does not necessarily restrict the delivery of a recombinant nucleic acid molecule only to the target cell and no other cell, but indicates that the delivery of the recombinant molecule, the expression of the recombinant molecule, or both, are specifically directed to a preselected host cell. Targeting delivery vehicles, including liposomes and viral vector systems are known in the art. For example, a liposome can be directed to a particular target cell or tissue by using a targeting agent, such as an antibody, soluble receptor or ligand, incorporated with the liposome, to target a particular cell or tissue to which the targeting molecule can bind. Targeting liposomes are described, for example, in Ho et al., 1986, Biochemistry 25: 5500-6; Ho et al., 1987a, J Biol Chem 262: 13979-84; Ho et al., 1987b, J Biol Chem 262: 13973-8; and U.S. Pat. No. 4,957,735 to Huang et al., each of which is incorporated herein by reference in its entirety). Ways in which viral vectors can be modified to deliver a nucleic acid molecule to a target cell have been discussed above. Alternatively, the route of administration, as discussed below, can be used to target a specific cell or tissue. For example, intracoronary administration of an adenoviral vector has been shown to be effective for the delivery of a gene cardiac myocytes (Maurice et al., 1999, J Clin. Invest. 104:21-29). Intravenous delivery of cholesterol-containing cationic liposomes has been shown to preferentially target pulmonary tissues (Liu et al., Nature Biotechnology 15:167, 1997), and effectively mediate transfer and expression of genes in vivo. Other examples of successful targeted in vivo delivery of nucleic acid molecules are known in the art. Finally, a recombinant nucleic acid molecule can be selectively (i.e., preferentially, substantially exclusively) expressed in a target cell by selecting a transcription control sequence, and preferably, a promoter, which is selectively induced in the target cell and remains substantially inactive in non-target cells.

According to the method of the present invention, a host cell is preferably transfected in vivo (i.e., in a mammal) as a result of administration to a mammal of a recombinant nucleic acid molecule, or ex vivo, by removing cells from a mammal and transfecting the cells with a recombinant nucleic acid molecule ex vivo. Transfection of a nucleic acid molecule into a host cell according to the present invention can be accomplished by any method by which a nucleic acid molecule administered into the cell in vivo, and includes, but is not limited to, transfection, electroporation, microinjection, lipofection, adsorption, viral infection, naked DNA injection and protoplast fusion. Methods of administration are discussed in detail below.

In one embodiment of the present invention, a recombinant nucleic acid molecule of the present invention is administered to a patient in a liposome delivery vehicle, whereby the nucleic acid sequence encoding the biomarker protein enters the host cell (i.e., the target cell) by lipofection. A liposome delivery vehicle contains the recombinant nucleic acid molecule and delivers the molecules to a suitable site in a host recipient. According to the present invention, a liposome delivery vehicle comprises a lipid composition that is capable of delivering a recombinant nucleic acid molecule of the present invention, including both plasmids and viral vectors, to a suitable cell and/or tissue in a patient. A liposome delivery vehicle of the present invention comprises a lipid composition that is capable of fusing with the plasma membrane of the target cell to deliver the recombinant nucleic acid molecule into a cell. A liposome delivery vehicle can also be used to deliver a protein, drug, or other regulatory compound to a patient.

A liposome delivery vehicle of the present invention can be modified to target a particular site in a mammal (i.e., a targeting liposome), thereby targeting and making use of a nucleic acid molecule of the present invention at that site. Suitable modifications include manipulating the chemical formula of the lipid portion of the delivery vehicle. Manipulating the chemical formula of the lipid portion of the delivery vehicle can elicit the extracellular or intracellular targeting of the delivery vehicle.° For example, a chemical can be added to the lipid formula of a liposome that alters the charge of the lipid bilayer of the liposome so that the liposome fuses with particular cells having particular charge characteristics. Other targeting mechanisms include targeting a site by addition of exogenous targeting molecules (i.e., targeting agents) to a liposome (e.g., antibodies, soluble receptors or ligands).

A liposome delivery vehicle is preferably capable of remaining stable in a patient for a sufficient amount of time to deliver a nucleic acid molecule of the present invention to a preferred site in the patient (i.e., a target cell). A liposome delivery vehicle of the present invention is preferably stable in the patient into which it has been administered for at least about 30 minutes, more preferably for at least about 1 hour and even more preferably for at least about 24 hours. A preferred liposome delivery vehicle of the present invention is from about 0.01 microns to about 1 microns in size.

Suitable liposomes for use with the present invention include any liposome. Preferred liposomes of the present invention include those liposomes commonly used in, for example, gene delivery methods known to those of skill in the art. Preferred liposome delivery vehicles comprise multilamellar vesicle (MLV) lipids and extruded lipids. Methods for preparation of MLV's are well known in the art. According to the present invention, “extruded lipids” are lipids which are prepared similarly to MLV lipids, but which are subsequently extruded through filters of decreasing size, as described in Templeton et al., 1997, Nature Biotech., 15:647-652, which is incorporated herein by reference in its entirety. Small unilamellar vesicle (SUV) lipids can also be used in the composition and method of the present invention. In one embodiment, liposome delivery vehicles comprise liposomes having a polycationic lipid composition (i.e., cationic liposomes) and/or liposomes having a cholesterol backbone conjugated to polyethylene glycol. In a preferred embodiment, liposome delivery vehicles useful in the present invention comprise one or more lipids selected from the group of DOTMA, DOTAP, DOTIM, DDAB, and cholesterol.

Preferably, the transfection efficiency of a nucleic acid:liposome complex of the present invention is at least about 1 picogram (pg) of protein expressed per milligram (mg) of total tissue protein per microgram (μg) of nucleic acid delivered. More preferably, the transfection efficiency of a nucleic acid:liposome complex of the present invention is at least about 10 pg of protein expressed per mg of total tissue protein per μg of nucleic acid delivered; and even more preferably, at least about 50 pg of protein expressed per mg of total tissue protein per μg of nucleic acid delivered; and most preferably, at least about 100 pg of protein expressed per mg of total tissue protein per μg of nucleic acid delivered.

Complexing a liposome with a nucleic acid molecule of the present invention can be achieved using methods standard in the art. A suitable concentration of a nucleic acid molecule of the present invention to add to a liposome includes a concentration effective for delivering a sufficient amount of recombinant nucleic acid molecule into a target cell of a patient such that the biomarker protein encoded by the nucleic acid molecule can be expressed in a an amount effective to inhibit the growth of the target cell or to inhibit or promote angiogenesis at a tissue site. Preferably, from about 0.1 μg to about 10 μg of nucleic acid molecule of the present invention is combined with about 8 nmol liposomes. In one embodiment, the ratio of nucleic acids to lipids (μg nucleic acid:nmol lipids) in a composition of the present invention is preferably at least from about 1:10 to about 6:1 nucleic acid:lipid by weight (i.e., 1:10=1 μg nucleic acid:10 nmol lipid).

According to the present invention, a regulatory compound for regulating the expression or biological activity of a biomarker, including a recombinant nucleic acid molecule encoding the biomarker, is typically administered to a patient in a composition. In addition to the recombinant nucleic acid molecule or other biomarker regulatory compound (i.e., a protein, antibody, carbohydrate, small molecule product of drug design), the composition can include, for example, a pharmaceutically acceptable carrier, which includes pharmaceutically acceptable excipients and/or delivery vehicles, for delivering the recombinant nucleic acid molecule or other regulatory compound to a patient (e.g., a liposome delivery vehicle). As used herein, a pharmaceutically acceptable carrier refers to any substance suitable for delivering a therapeutic composition useful in the method of the present invention to a suitable in vivo or ex vivo site. Preferred pharmaceutically acceptable carriers are capable of maintaining a recombinant nucleic acid molecule of the present invention in a form that, upon arrival of the nucleic acid molecule to a target cell, the nucleic acid molecule is capable of entering the cell and being expressed by the cell. Suitable excipients of the present invention include excipients or formularies that transport or help transport, but do not specifically target a nucleic acid molecule to a cell (also referred to herein as non-targeting carriers). Examples of pharmaceutically acceptable excipients include, but are not limited to water, phosphate buffered saline, Ringer's solution, dextrose solution, serum-containing solutions, Hank's solution, other aqueous physiologically balanced solutions, oils, esters and glycols. Aqueous carriers can contain suitable auxiliary substances required to approximate the physiological conditions of the recipient, for example, by enhancing chemical stability and isotonicity.

Suitable auxiliary substances include, for example, sodium acetate, sodium chloride, sodium lactate, potassium chloride, calcium chloride, and other substances used to produce phosphate buffer, Tris buffer, and bicarbonate buffer. Auxiliary substances can also include preservatives, such as thimerosal, m- or o-cresol, formalin and benzol alcohol. Compositions of the present invention can be sterilized by conventional methods and/or lyophilized.

One type of pharmaceutically acceptable carrier includes a controlled release formulation that is capable of slowly releasing a composition of the present invention into an animal. As used herein, a controlled release formulation comprises recombinant nucleic acid molecule or other biomarker regulatory compound of the present invention in a controlled release vehicle. Suitable controlled release vehicles include, but are not limited to, biocompatible polymers, other polymeric matrices, capsules, microcapsules, microparticles, bolus preparations, osmotic pumps, diffusion devices, liposomes, lipospheres, and transdermal delivery systems. Suitable delivery vehicles have been previously described herein, and include, but are not limited to liposomes, viral vectors or other delivery vehicles, including ribozymes. Natural lipid-containing delivery vehicles include cells and cellular membranes. Artificial lipid-containing delivery vehicles include liposomes and micelles. As discussed above, a delivery vehicle of the present invention can be modified to target to a particular site in a patient, thereby targeting and making use of a nucleic acid molecule at that site. Suitable modifications include manipulating the chemical formula of the lipid portion of the delivery vehicle and/or introducing into the vehicle a targeting agent capable of specifically targeting a delivery vehicle to a preferred site, for example, a preferred cell type. Other suitable delivery vehicles include gold particles, poly-L-lysine/DNA-molecular conjugates, and artificial chromosomes.

As discussed above, a composition of the present invention is administered to a patient in a manner effective to deliver the recombinant nucleic acid molecule comprising a nucleic acid sequence encoding a biomarker protein to a target cell, whereby the target cell is transfected by the recombinant molecule and whereby the biomarker protein is expressed in the target cell. When a biomarker regulatory compound is to be delivered to a target cell in a patient, the composition is administered in a manner effective to deliver the biomarker regulatory compound to the target cell, whereby the compound can act on the cell (e.g., enter the cell and act on the biomarker or an inhibitor or stimulator thereof) so that the expression or biological activity of the biomarker is increased or decreased, depending on the isoform and the goal of the therapy. Suitable administration protocols include any in vivo or ex vivo administration protocol.

According to the present invention, an effective administration protocol (i.e., administering a composition of the present invention in an effective manner) comprises suitable dose parameters and modes of administration that result in transfection and expression of a recombinant nucleic acid molecule encoding a biomarker protein or another biomarker regulatory compound, in a target cell of a patient, and subsequent inhibition of the growth of the target cell or inhibition or promotion of angiogenesis, preferably so that the patient obtains some measurable, observable or perceived benefit from such administration. In some situations, where the target cell population is accessible for sampling, effective dose parameters can be determined using methods as described herein for assessment of tumor growth or using methods known in the art for the assessment of angiogenesis. Such methods include removing a sample of the target cell population from the patient prior to and after the recombinant nucleic acid molecule is administered, and measuring changes in biomarker expression or biological activity, as well as measuring inhibition of the cell or impact on angiogenesis of a suitable cell line. Alternatively, effective dose parameters can be determined by experimentation using in vitro cell cultures, in vivo animal models, and eventually, clinical trials if the patient is human. Effective dose parameters can be determined using methods standard in the art for a particular disease or condition that the patient has or is at risk of developing. Such methods include, for example, determination of survival rates, side effects (i.e., toxicity) and progression or regression of disease.

According to the present invention, suitable methods of administering a composition comprising a recombinant nucleic acid molecule of the present invention to a patient include any route of in vivo administration that is suitable for delivering a recombinant nucleic acid molecule into a patient. The preferred routes of administration will be apparent to those of skill in the art, depending on the type of delivery vehicle used, the target cell population, whether the compound is a protein, nucleic acid, or other compound (e.g., a drug) and the disease or condition experienced by the patient. Preferred methods of in vivo administration include, but are not limited to, intravenous administration, intraperitoneal administration, intramuscular administration, intracoronary administration, intraarterial administration (e.g., into a carotid artery), subcutaneous administration, transdermal delivery, intratracheal administration, subcutaneous administration, intraarticular administration, intraventricular administration, inhalation (e.g., aerosol), intracerebral, nasal, oral, pulmonary administration, impregnation of a catheter, and direct injection into a tissue. In an embodiment where the target cells are in or near a tumor, a preferred route of administration is by direct injection into the tumor or tissue surrounding the tumor. For example, when the tumor is a breast tumor, the preferred methods of administration include impregnation of a catheter, and direct injection into the tumor.

Intravenous, intraperitoneal, and intramuscular administrations can be performed using methods standard in the art. Aerosol (inhalation) delivery can also be performed using methods standard in the art (see, for example, Stribling et al., Proc. Natl. Acad. Sci. USA 189:11277-11281, 1992, which is incorporated herein by reference in its entirety). Oral delivery can be performed by complexing a therapeutic composition of the present invention to a carrier capable of withstanding degradation by digestive enzymes in the gut of an animal. Examples of such carriers, include plastic capsules or tablets, such as those known in the art.

One method of local administration is by direct injection. Direct injection techniques are particularly useful for administering a recombinant nucleic acid molecule to a cell or tissue that is accessible by surgery, and particularly, on or near the surface of the body. Administration of a composition locally within the area of a target cell refers to injecting the composition centimeters and preferably, millimeters from the target cell or tissue.

Various methods of administration and delivery vehicles disclosed herein have been shown to be effective for delivery of a nucleic acid molecule to a target cell, whereby the nucleic acid molecule transfected the cell and was expressed. In many studies, successful delivery and expression of a heterologous gene was achieved in preferred cell types and/or using preferred delivery vehicles and routes of administration of the present invention. All of the publications discussed below and elsewhere herein with regard to gene delivery and delivery vehicles are incorporated herein by reference in their entirety. For example, using liposome delivery, U.S. Pat. No. 5,705,151, issued Jan. 6, 1998, to Dow et al. demonstrated the successful in vivo intravenous delivery of a nucleic acid molecule encoding a superantigen and a nucleic acid molecule encoding a cytokine in a cationic liposome delivery vehicle, whereby the encoded proteins were expressed in tissues of the animal, and particularly in pulmonary tissues. Dow et al. also demonstrated successful in vivo delivery of a nucleic acid molecule by direct injection into a site of a tumor. As discussed above, Liu et al., 1997, ibid. demonstrated that intravenous delivery of cholesterol-containing cationic liposomes containing genes preferentially targets pulmonary tissues and effectively mediates transfer and expression of the genes in vivo. Several publications by Dzau and collaborators demonstrate the successful in vivo delivery and expression of a gene into cells of the heart, including cardiac myocytes and fibroblasts and vascular smooth muscle cells using both naked DNA and Hemagglutinating virus of Japan-liposome delivery, administered by both incubation within the pericardium and infusion into a coronary artery (intracoronary delivery) (See, for example, Aoki et al., 1997, J Mol. Cell, Cardiol. 29:949-959; Kaneda et al., 1997, Ann N.Y. Acad. Sci. 811:299-308; and von der Leyen et al., 1995, Proc Natl Acad Sci USA 92:1137-1141).

As discussed above, delivery of numerous nucleic acid sequences has been accomplished by administration of viral vectors encoding the nucleic acid sequences. Using such vectors, successful delivery and expression has been achieved using ex vivo delivery (See, of many examples, retroviral vector; Blaese et al., 1995, Science 270:475-480; Bordignon et al., 1995, Science 270:470-475), nasal administration (CFTR-adenovirus-associated vector), intracoronary administration (adenoviral vector and Hemagglutinating virus of Japan, see above), intravenous administration (adeno-associated viral vector; Koeberl et al., 1997, Proc Natl Acad Sci USA 94:1426-1431). A publication by Maurice et al., 1999, ibid. demonstrated that an adenoviral vector encoding a β2-adrenergic receptor, administered by intracoronary delivery, resulted in diffuse multichamber myocardial expression of the gene in vivo, and subsequent significant increases in hemodynamic function and other improved physiological parameters. Levine et al. describe in vitro, ex vivo and in vivo delivery and expression of a gene to human adipocytes and rabbit adipocytes using an adenoviral vector and direct injection of the constructs into adipose tissue (Levine et al., 1998, J. Nutr. Sci. Vitaminol. 44:569-572).

In the area of neuronal gene delivery, multiple successful in vivo gene transfers have been reported. Millecamps et al. reported the targeting of adenoviral vectors to neurons using neuron restrictive enhancer elements placed upstream of the promoter for the transgene (phosphoglycerate promoter). Such vectors were administered to mice and rats intramuscularly and intracerebrally, respectively, resulting in successful neuronal-specific transfection and expression of the transgene in vivo (Millecamps et al., 1999, Nat. Biotechnol. 17:865-869). As discussed above, Bennett et al. reported the use of adeno-associated viral vector to deliver and express a gene by subretinal injection in the neural retina in vivo for greater than 1 year (Bennett, 1999, ibid.).

Gene delivery to synovial lining cells and articular joints has had similar successes. Oligino and colleagues report the use of a herpes simplex viral vector that is deficient for the immediate early genes, ICP4, 22 and 27, to deliver and express two different receptors in synovial lining cells in vivo (Oligino et al., 1999, Gene Ther. 6:1713-1720). The herpes vectors were administered by intraarticular injection. Kuboki et al. used adenoviral vector-mediated gene transfer and intraarticular injection to successfully and specifically express a gene in the temporomandibular joints of guinea pigs in vivo (Kuboki et al., 1999, Arch. Oral. Biol. 44:701-709). Apparailly and colleagues systemically administered adenoviral vectors encoding IL-10 to mice and demonstrated successful expression of the gene product and profound therapeutic effects in the treatment of experimentally induced arthritis (Apparailly et al., 1998, J Immunol. 160:5213-5220). In another study, murine leukemia virus-based retroviral vector was used to deliver (by intraarticular injection) and express a human growth hormone gene both ex vivo and in vivo (Ghivizzani et al., 1997, Gene Ther. 4:977-982). This study showed that expression by in vivo gene transfer was at least equivalent to that of the ex vivo gene transfer. As discussed above, Sawchuk et al. has reported successful in vivo adenoviral vector delivery of a gene by intraarticular injection, and prolonged expression of the gene in the synovium by pretreatment of the joint with anti-T cell receptor monoclonal antibody (Sawchuk et al., 1996, ibid. Finally, it is noted that ex vivo gene transfer of human interleukin-1 receptor antagonist using a retrovirus has produced high level intraarticular expression and therapeutic efficacy in treatment of arthritis, and is now entering FDA approved human gene therapy trials (Evans and Robbins, 1996, Curr. Opin. Rheumatol. 8:230-234). Therefore, the state of the art in gene therapy has led the FDA to consider human gene therapy an appropriate strategy for the treatment of at least arthritis. Taken together, all of the above studies in gene therapy indicate that delivery and expression of an biomarker-encoding recombinant nucleic acid molecule according to the present invention is feasible.

Another method of delivery of recombinant molecules is in a non-targeting carrier (e.g., as “naked” DNA molecules, such as is taught, for example in Wolff et al., 1990, Science 247, 1465-1468). Such recombinant nucleic acid molecules are typically injected by direct or intramuscular administration. Recombinant nucleic acid molecules to be administered by naked DNA administration include a nucleic acid molecule of the present invention, and preferably includes a recombinant molecule of the present invention that preferably is replication, or otherwise amplification, competent. A naked nucleic acid reagent of the present invention can comprise one or more nucleic acid molecule of the present invention in the form of, for example, a dicistronic recombinant molecule. Naked nucleic acid delivery can include intramuscular, subcutaneous, intradermal, transdermal, intranasal and oral routes of administration, with direct injection into the target tissue being most preferred. A preferred single dose of a naked nucleic acid vaccine ranges from about 1 nanogram (ng) to about 100 μg, depending on the route of administration and/or method of delivery, as can be determined by those skilled in the art. Suitable delivery methods include, for example, by injection, as drops, aerosolized and/or topically. In one embodiment, pure DNA constructs cover the surface of gold particles (1 to 3 μm in diameter) and are propelled into skin cells or muscle with a “gene gun.”

In accordance with the present invention, a suitable single dose of a recombinant nucleic acid molecule encoding a biomarker protein as described herein is a dose that is capable of transfecting a host cell and being expressed in the host cell at a level sufficient, in the absence of the addition of any other factors or other manipulation of the host cell, to regulate angiogenesis and/or the tumorigenicity of the host cell when administered one or more times over a suitable time period. Doses can vary depending upon the cell type being targeted, the route of administration, the delivery vehicle used, and the disease or condition being treated.

In one embodiment, an appropriate single dose of a nucleic acid:liposome complex of the present invention is from about 0.1 μg to about 100 μg per kg body weight of the patient to which the complex is being administered. In another embodiment, an appropriate single dose is from about 1 μg to about 10 μg per kg body weight. In another embodiment, an appropriate single dose of nucleic acid:lipid complex is at least about 0.1 μg of nucleic acid, more preferably at least about 1 μg of nucleic acid, even more preferably at least about 10 μg of nucleic acid, even more preferably at least about 50 μg of nucleic acid, and even more preferably at least about 100 μg of nucleic acid.

Preferably, an appropriate single dose of a recombinant nucleic acid molecule encoding a biomarker protein of the present invention results in at least about 1 pg of protein expressed per mg of total tissue protein per μg of nucleic acid delivered. More preferably, an appropriate single dose is a dose which results in at least about 10 pg of protein expressed per mg of total tissue protein per μg of nucleic acid delivered; and even more preferably, at least about 50 pg of protein expressed per mg of total tissue protein per μg of nucleic acid delivered; and most preferably, at least about 100 pg of protein expressed per mg of total tissue protein per μg of nucleic acid delivered.

When the biomarker regulatory agent is a protein, small molecule (i.e., the products of drug design) or antibody, a preferred single dose of such a compound typically comprises between about 0.01 microgram×kilogram⁻¹ and about 10 milligram×kilogram⁻¹ body weight of an animal. A more preferred single dose of an agent comprises between about 1 microgram×kilogram⁻¹ and about 10 milligram×kilograms⁻¹ body weight of an animal. An even more preferred single dose of an agent comprises between about 5 microgram ×kilograms⁻¹ and about 7 milligram×kilograms⁻¹ body weight of an animal. An even more preferred single dose of an agent comprises between about 10 microgram×kilogram⁻¹ and about 5 milligram×kilograms⁻¹ body weight of an animal. Another particularly preferred single dose of an agent comprises between about 0.1 microgram×kilograms⁻¹ and about 10 microgram×kilograms⁻¹ body weight of an animal, if the agent is delivered parenterally.

In another embodiment, a targeting vector can be used to deliver a particular nucleic acid molecule into a recombinant host cell, wherein the nucleic acid molecule is used to delete or inactivate an endogenous gene (e.g., biomarker-encoding gene) within the host cell or microorganism (i.e., used for targeted gene disruption or knock-out technology). Such a vector may also be known in the art as a “knock-out” vector. In one aspect of this embodiment, a portion of the vector, but more typically, the nucleic acid molecule inserted into the vector (i.e., the insert), has a nucleic acid sequence that is homologous to a nucleic acid sequence of a target gene in the host cell (i.e., a gene which is targeted to be deleted or inactivated). The nucleic acid sequence of the vector insert is designed to bind to the target gene such that the target gene and the insert undergo homologous recombination, whereby the endogenous target gene is deleted, inactivated or attenuated (i.e., by at least a portion of the endogenous target gene being mutated or deleted).

Compositions of the present invention can be administered to any mammalian patient, and preferably to humans. According to the present invention, administration of a composition is useful to inhibit the tumorigenicity of a target cell or to treat cancer, or to inhibit angiogenesis in a tissue of a patient. Typically, it is desirable to inhibit the growth of a target cell, or to reduce tumor burden in the patient (tumor numbers and/or volume), or to prevent further growth of the tumor in the patient (tumor stasis), or to obtain any therapeutic benefit in the patient (e.g., increased survival). In one embodiment, patients whom are suitable candidates for the method of the present invention include, but are not limited to, patients that have, or are at risk of developing (e.g., are predisposed to), cancer or a lymphoproliferative disease, or any condition in which regulation of angiogenesis might be beneficial. In another embodiment, patients whom are suitable candidates for a method of the invention include, but are not limited to: patients with vascular deficiencies, cardiovascular disease, or patients in whom stimulation of endothelial cell activation and stabilization of newly formed microvessels or other vessels would be beneficial. Increasing or decreasing the expression or biological activity of various biomarkers to inhibit or promote angiogenesis in the absence of obtaining some therapeutic benefit is useful for the purposes of determining factors involved (or not involved) in a disease and preparing a patient to more beneficially receive another therapeutic composition. In a preferred embodiment, however, the methods of the present invention are directed to the inhibition of cancer or inhibition or promotion of angiogenesis in a tissue, which is useful in providing some therapeutic benefit to a patient.

As such, a therapeutic benefit is not necessarily a cure for a particular disease or condition, but rather, preferably encompasses a result which most typically includes alleviation of the disease or condition or increased survival, elimination of the disease or condition, reduction of a symptom associated with the disease or condition (e.g. reduced tumor burden), prevention or alleviation of a secondary disease or condition resulting from the occurrence of a primary disease or condition (e.g., metastatic tumor growth resulting from a primary cancer), and/or prevention of the disease or condition. As used herein, the phrase “protected from a disease” refers to reducing the symptoms of the disease; reducing the occurrence of the disease, and/or reducing the severity of the disease. Protecting a patient can refer to the ability of a composition of the present invention, when administered to a patient, to prevent a disease from occurring and/or to cure or to alleviate disease symptoms, signs or causes. As such, to protect a patient from a disease includes both preventing disease occurrence (prophylactic treatment) and treating a patient that has a disease (therapeutic treatment). In particular, protecting a patient from a disease is accomplished by inhibiting the tumorigenicity of a target cell in the patient or inhibiting or promoting angiogenesis in the cells or tissues of a patient by regulating biomarker expression or biological activity such that a beneficial effect is obtained. A beneficial effect can easily be assessed by one of ordinary skill in the art and/or by a trained clinician who is treating the patient. The term, “disease” refers to any deviation from the normal health of a mammal and includes a state when disease symptoms are present, as well as conditions in which a deviation (e.g., infection, gene mutation, genetic defect, etc.) has occurred, but symptoms are not yet manifested.

One embodiment of the present invention relates to a method (i.e., an assay) for diagnosing or assessing tumor cells (cancer) or the potential therefore in a patient. In one aspect of this embodiment, the method includes the steps of: (a) detecting a level of expression or activity of one or more biomarkers of the present invention in a test sample from a patient to be diagnosed; and (b) comparing the level of expression or activity of the biomarker(s) in the test sample to a normal level of biomarker expression or activity established from a control sample. For example, it is noted that the present inventor has determined that expression of MAGP-2 is upregulated in uterine tumor cells. According to the present invention, detection of the biomarker can be achieved by any method that detects the expression of the biomarker. Detection of a statistically significant difference in biomarker expression or activity in the test sample, as compared to the control level of biomarker expression or biological activity, is an indicator of a difference in the tumorigenicity or potential therefore of cells in the test sample as compared to cells in the control sample. The expression of the biomarker may be cell- and context-specific. Therefore, biomarker expression or activity could be either upregulated or downregulated in a cell as compared to the control. Typically, the biomarker is upregulated or downregulated in the manner associated with the expression of the biomarker during angiogenesis as represented in any one or more of the Tables or experiments described herein. The method of the present invention can be used for any type of tumor wherein the biomarker expression or activity is found to be statistically significantly changed in tumor cells as compared to the corresponding normal cells.

According to the present invention, the phrase “tumorigenicity” refers primarily to the tumor status of a cell or cells (e.g., the extent of neoplastic transformation of a cell, the malignancy of a cell, the propensity for a cell to form a tumor and/or have characteristics of a tumor, or simply the presence or absence of tumor cells in a patient or tissue/organ), which is reflective of a change of a cell or population of cells from a normal to malignant state. Tumorigenicity indicates that tumor cells are present in a sample, and/or that the transformation of cells from normal to tumor cells is in progress, as may be confirmed by any standard of measurement of tumor development. The change typically involves cellular proliferation at a rate which is more rapid than the growth observed for normal cells under the same conditions, and which is typically characterized by one or more of the following traits: continued growth even after the instigating factor (e.g., carcinogen, virus) is no longer present; a lack of structural organization and/or coordination with normal tissue, and typically, a formation of a mass of tissue, or tumor. A tumor, therefore, is most generally described as a proliferation of cells (e.g., a neoplasia, a growth, a polyp) resulting from neoplastic growth and is most typically a malignant tumor. In the case of a neoplastic transformation, a neoplasia is malignant or is predisposed to become malignant. Malignant tumors are typically characterized as being anaplastic (primitive cellular growth characterized by a lack of differentiation), invasive (moves into and destroys surrounding tissues) and/or metastatic (spreads to other parts of the body). As used herein, reference to a “potential for neoplastic transformation”, “potential for tumorigenicity” or a “potential for tumor cell growth” refers to an expectation or likelihood that, at some point in the future, a cell or population of cells will display characteristics of neoplastic transformation, including rapid cellular proliferation characterized by anaplastic, invasive and/or metastatic growth.

This method of the present invention has several different uses. First, the method can be used to diagnose tumorigenicity, or the potential for tumorigenicity, or simply the presence or absence of tumor cells, in a subject. The subject can be an individual who is suspected of having a tumor, or an individual who is presumed to be healthy, but who is undergoing a routine or diagnostic screening for the presence of a tumor (cancer). The subject can also be an individual who has previously been diagnosed with cancer and treated, and who is now under surveillance for recurring tumor growth. The terms “diagnose”, “diagnosis”, “diagnosing” and variants thereof refer to the identification of a disease or condition on the basis of its signs and symptoms. As used herein, a “positive diagnosis” indicates that the disease or condition, or a potential for developing the disease or condition, has been identified. In contrast, a “negative diagnosis” indicates that the disease or condition, or a potential for developing the disease or condition, has not been identified. Therefore, in the present invention, a positive diagnosis (i.e., a positive assessment) of tumor growth or tumorigenicity (i.e., malignant or inappropriate cell growth or neoplastic transformation), or the potential therefore, means that the indicators (e.g., signs, symptoms) of tumor presence and/or growth according to the present invention (i.e., a change in biomarker expression or biological activity as compared to a baseline control) have been identified in the sample obtained from the subject. Such a subject can then be prescribed treatment to reduce or eliminate the tumor growth. Similarly, a negative diagnosis (i.e., a negative assessment) for tumor growth or a potential therefore or the absence of tumor cells means that the indicators of tumor growth or tumor presence or a likelihood of developing tumors as described herein (i.e., a change in biomarker expression or biological activity as compared to a baseline control) have not been identified in the sample obtained from the subject. In this instance, the subject is typically not prescribed any treatment, but may be reevaluated at one or more timepoints in the future to again assess tumor growth. Baseline levels for this particular embodiment of the method of assessment of tumorigenicity of the present invention are typically based on a “normal” or “healthy” sample from the same bodily source as the test sample (i.e., the same tissue, cells or bodily fluid), as discussed in detail below.

In a second embodiment, the method of the present invention can be used more specifically to “stage” a tumor in a patient. Therefore, the patient can be diagnosed as having a tumor or. potential therefore by the method as discussed above, or by any other suitable method (e.g., physical exam, X-ray, CT scan, blood test for a tumor antigen, surgery), and then (or at the same time, when the present method is also used as a diagnostic), the method of the present invention can be used to determine the stage of progression of tumor growth in an individual. For most cancer types, standard staging criteria exist and are known in the art. For example, in breast tumors, there are five different general stages of tumor development which are known and acknowledged in the art as stages 0, I, II, III and IV (although these stages can be grouped into more complex subgroups based on more specific indicators). In this embodiment of the method of the present invention, the biomarker expression and/or biological activity in the patient sample is compared to a panel of several different “baseline” levels of biomarker expression or biological activity, wherein each baseline level represents a previously established level for a given stage of the cancer being diagnosed. The ability to “stage” a tumor in the method of the present invention allows the physician to more appropriately prescribe treatment for the patient.

In a third embodiment of this method of the present invention, the method is used to monitor the success, or lack thereof, of a treatment for cancer in a patient that has been diagnosed as having cancer. In this embodiment, the baseline or control level of biomarker expression or biological activity typically includes the previous level of biomarker expression or biological activity in a sample of the patient's tumor, so that a new level of biomarker expression or biological activity can be compared to determine whether tumor cell growth is decreasing, increasing, or substantially unchanged as compared to the previous, or first sample (i.e., the initial sample which presented a positive diagnosis). In addition, or alternatively, a baseline established as a “normal” or “healthy” level of biomarker expression or biological activity can be used in this embodiment, particularly to determine in what manner the biomarker expression is regulated in tumors for the given cell type. This embodiment allows the physician to monitor the success, or lack of success, of a treatment that the patient is receiving for cancer, and can help the physician to determine whether the treatment should be modified. In one embodiment of the present invention, the method includes additional steps of modifying cancer treatment for the patient based on whether an increase or decrease in tumor cell growth is indicated by evaluation of biomarker expression and/or biological activity in the patient.

The first step of the method of the present invention includes detecting biomarker expression or biological activity in a test sample from a patient. According to the present invention, the term “test sample” can be used generally to refer to a sample of any type which contains cells or products that have been secreted from cells (e.g., some biomarkers of the invention are secreted proteins and so one can evaluate a cell supemate, bodily fluid or other media into which such biomarkers may have been secreted by a cell) to be evaluated by the present method, including but not limited to, a sample of isolated cells, a tissue sample and/or a bodily fluid sample. According to the present invention, a sample of isolated cells is a specimen of cells, typically in suspension or separated from connective tissue which may have connected the cells within a tissue in vivo, which have been collected from an organ, tissue or fluid by any suitable method which results in the collection of a suitable number of cells for evaluation by the method of the present invention. The cells in the cell sample are not necessarily of the same type, although purification methods can be used to enrich for the type of cells that are preferably evaluated. Cells can be obtained, for example, by scraping of a tissue, processing of a tissue sample to release individual cells, or isolation from a bodily fluid. A tissue sample, although similar to a sample of isolated cells, is defined herein as a section of an organ or tissue of the body which typically includes several cell types and/or cytoskeletal structure which holds the cells together. One of skill in the art will appreciate that the term “tissue sample” may be used, in some instances, interchangeably with a “cell sample”, although it is preferably used to designate a more complex structure than a cell sample. A tissue sample can be obtained by a biopsy, for example, including by cutting, slicing, or a punch. A bodily fluid sample, like the tissue sample, contains the cells to be evaluated for biomarker expression or biological activity and/or contains the soluble biomarker secreted by cells, and is a fluid obtained by any method suitable for the particular bodily fluid to be sampled. Bodily fluids suitable for sampling include, but are not limited to, blood, mucous, seminal fluid, saliva, breast milk, bile and urine.

In general, the sample type (i.e., cell, tissue or bodily fluid) is selected based on the accessibility and structure of the organ or tissue to be evaluated for tumor cell growth and/or on what type of cancer is to be evaluated. For example, if the organ/tissue to be evaluated is the breast, the sample can be a sample of epithelial cells from a biopsy (i.e., a cell sample) or a breast tissue sample from a biopsy (a tissue sample). The sample that is most useful in the present invention will be cells, tissues or bodily fluids isolated from a patient by a biopsy or surgery or routine laboratory fluid collection.

Once a sample is obtained from the patient, the sample is evaluated for detection of biomarker expression or biological activity in the cells of the sample. The phrase “biomarker expression” can generally refer to biomarker mRNA transcription or biomarker protein translation. Preferably, the method of detecting biomarker expression or biological activity in the patient is the same or qualitatively equivalent to the method used for detection of biomarker expression or biological activity in the sample used to establish the baseline level.

Methods suitable for detecting biomarker transcription include any suitable method for detecting and/or measuring mRNA levels from a cell or cell extract. Such methods include, but are not limited to: polymerase chain reaction (PCR), reverse transcriptase PCR (RT-PCR), in situ hybridization, Northern blot, sequence analysis, gene microarray analysis (gene chip analysis) and detection of a reporter gene. Such methods for detection of transcription levels are well known in the art, and many of such methods are described in detail in the attached examples, in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Labs Press, 1989 and/or in Glick et al., Molecular Biotechnology: Principles and Applications of Recombinant DNA, ASM Press, 1998; Sambrook et al., ibid., and Glick et al., ibid. are incorporated by reference herein in their entireties.

Measurement of biomarker transcription is suitable when the sample is a cell or tissue sample; therefore, when the sample is a bodily fluid sample containing cells or cellular extracts, the cells are typically isolated from the bodily fluid to perform the expression assay, or the fluid is evaluated for the presence of secreted biomarker protein.

Biomarker expression can also be identified by detection of biomarker translation (i.e., detection of biomarker protein in a sample). Methods suitable for the detection of biomarker protein include any suitable method for detecting and/or measuring proteins from a cell or cell extract. Such methods include, but are not limited to, immunoblot (e.g., Western blot), enzyme-linked immunosorbant assay (ELISA), radioimmunoassay (RIA), immunoprecipitation, immunohistochemistry and immunofluorescence. Particularly preferred methods for detection of proteins include any single-cell assay, including immunohistochemistry and immunofluorescence assays. Such methods are well known in the art. Furthermore, antibodies against certain of the biomarkers described herein are known in the art and are described in the public literature, and methods for production of antibodies that can be developed against biomarkers are well known in the art.

The method of the present invention includes a step of comparing the level of biomarker expression or biological activity detected in step (a) to a baseline level (also known as a control level) of biomarker expression or biological activity established from a control sample. According to the present invention, a “baseline level” is a control level, and in some embodiments (but not all embodiments, depending on the method), a normal level, of biomarker expression or activity against which a test level of biomarker expression or biological activity (i.e., in the test sample) can be compared. Therefore, it can be determined, based on the control or baseline level of biomarker expression or biological activity, whether a sample to be evaluated for tumor cell growth has a measurable increase, decrease, or substantially no change in biomarker expression or biological activity, as compared to the baseline level. As discussed above, the baseline level can be indicative of different states of cell tumorigenicity or lack thereof, depending on the primary use of the assay. For example, the baseline level can be indicative of the cell growth expected in a normal (i.e., healthy, negative control, non-tumor) cell sample. Therefore, the term “negative control” or “normal control” used in reference to a baseline level of biomarker expression or biological activity typically refers to a baseline level established in a sample from the patient or from a population of individuals which is believed to be normal (i.e., non-tumorous, not undergoing neoplastic transformation, not exhibiting inappropriate cell growth). For some biomarkers, the negative control may have a higher level of biomarker expression or activity than the tumor type. In another embodiment, a baseline can be indicative of a positive diagnosis of tumor cell growth. Such a baseline level, also referred to herein as a “positive control” baseline, refers to a level of biomarker expression or biological activity established in a cell sample from the patient, another patient, or a population of individuals, wherein the sample was believed, based on data for that cell sample, to be neoplastically transformed (i.e., tumorous, exhibiting inappropriate cell growth, cancerous). In one aspect, the baseline can be indicative of a particular stage of tumor cell growth, which will allow a patient's sample to be “staged” (i.e., the stage of the cancer in the patient can be identified). In yet another embodiment, the baseline level can be established from a previous sample from the patient being tested, so that the tumor growth of a patient can be monitored over time and/or so that the efficacy of a given therapeutic protocol can be evaluated over time. Methods for detecting biomarker expression or biological activity are described in detail above.

The method for establishing a baseline level of biomarker expression or activity is selected based on the sample type, the tissue or organ from which the sample is obtained, the status of the patient to be evaluated, and, as discussed above, the focus or goal of the assay (e.g., diagnosis, staging, monitoring). Preferably, the method is the same method that will be used to evaluate the sample in the patient. In a most preferred embodiment, the baseline level is established using the same cell type as the cell to be evaluated. Baseline levels can be established from an autologous control sample obtained from the patient. According to the present invention, and as used in the art, the term “autologous” means that the sample is obtained from the same patient from which the sample to be evaluated is obtained. The control sample should be of or from the same cell type and preferably, the control sample is obtained from the same organ, tissue or bodily fluid as the sample to be evaluated, such that the control sample serves as the best possible baseline for the sample to be evaluated. In one embodiment, when the goal of the assay is diagnosis of abnormal cell growth, it is desirable to take the control sample from a population of cells, a tissue or a bodily fluid which is believed to represent a “normal” cell, tissue, or bodily fluid, or at a minimum, a cell or tissue which is least likely to be undergoing or potentially be predisposed to develop tumor cell growth. For example, if the sample to be evaluated is an area of apparently abnormal cell growth, such as a tumorous mass, the control sample is preferably obtained from a section of apparently normal tissue (i.e., an area other than and preferably a reasonable distance from the tumorous mass) in the tissue or organ where the tumorous mass is growing.

In another embodiment, when the goal is to monitor tumor cell growth in the patient, the autologous baseline sample is typically a previous sample from the patient which was taken from an apparent or confirmed tumorous mass, and/or from apparently normal (i.e., non-tumor) tissue in the patient (or a different type of baseline for normal can be used, as discussed below). Therefore, a second method for establishing a baseline level of biomarker expression or biological activity is to establish a baseline level of biomarker expression or biological activity from at least one measurement of biomarker expression or biological activity in a previous sample from the same patient. Such a sample is also an autologous sample, but is taken from the patient at a different time point than the sample to be tested. Preferably, the previous sample(s) were of a same cell type, tissue type or bodily fluid type as the sample to be presently evaluated. In one embodiment, the previous sample resulted in a negative diagnosis (i.e., no tumor cell growth, or potential therefore, was identified). In this embodiment, a new sample is evaluated periodically (e.g., at annual physicals), and as long as the patient is determined to be negative for tumor development, an average or other suitable statistically appropriate baseline of the previous samples can be used as a “negative control” for subsequent evaluations. For the first evaluation, an alternate control can be used, as described below, or additional testing may be performed to confirm an initial negative diagnosis, if desired, and the value for biomarker expression or biological activity can be used thereafter. This type of baseline control is frequently used in other clinical diagnosis procedures where a “normal” level may differ from patient to patient and/or where obtaining an autologous control sample at the time of diagnosis is not possible, not practical or not beneficial.

In another embodiment, the previous sample from the patient resulted in a positive diagnosis (i.e., tumor growth was positively identified). In this embodiment, the baseline provided by the previous sample is effectively a positive control for tumor growth, and the subsequent samplings of the patient are compared to this baseline to monitor the progress of the tumor growth and/or to evaluate the efficacy of a treatment that is being prescribed for the cancer. In this embodiment, it may also be beneficial to have a negative baseline level of biomarker expression or biological activity (i.e., a normal cell baseline control), so that a baseline for remission or regression of the tumor can be set. Monitoring of a patient's tumor growth can be used by the clinician to modify cancer treatment for the patient based on whether an increase or decrease in cell growth is indicated.

It will be clear to those of skill in the art that some samples to be evaluated will not readily provide an obvious autologous control sample, or it may be determined that collection of autologous control samples is too invasive and/or causes undue discomfort to the patient. In these instances, an alternate method of establishing a baseline level of biomarker expression or biological activity can be used.

Another method for establishing a baseline level of biomarker expression or biological activity is to establish a baseline level of biomarker expression or biological activity from control samples, and preferably control samples that were obtained from a population of matched individuals. It is preferred that the control samples are of the same sample type as the sample type to be evaluated for biomarker expression or biological activity (e.g., the same cell type, and preferably from the same tissue or organ). According to the present invention, the phrase “matched individuals” refers to a matching of the control individuals on the basis of one or more characteristics which are suitable for the type of cell or tumor growth to be evaluated. For example, control individuals can be matched with the patient to be evaluated on the basis of gender, age, race, or any relevant biological or sociological factor that may affect the baseline of the control individuals and the patient (e.g., preexisting conditions, consumption of particular substances, levels of other biological or physiological factors). For example, levels of biomarker expression in the uterine tissue of a normal individual (i.e., having uterine tissue that is not neoplastically transformed or predisposed to such transformation) may be lower or higher in individuals of a given classification (e.g., elderly vs. teenagers, smokers vs. non-smokers) (although such variation in groups is not currently known). To establish a control or baseline level of biomarker expression or biological activity, samples from a number of matched individuals are obtained and evaluated for biomarker expression or biological activity. The sample type is preferably of the same sample type and obtained from the same organ, tissue or bodily fluid as the sample type to be evaluated in the test patient. The number of matched individuals from whom control samples must be obtained to establish a suitable control level (e.g., a population) can be determined by those of skill in the art, but should be statistically appropriate to establish a suitable baseline for comparison with the patient to be evaluated (i.e., the test patient). The values obtained from the control samples are statistically processed using any suitable method of statistical analysis to establish a suitable baseline level using methods standard in the art for establishing such values.

It will be appreciated by those of skill in the art that a baseline need not be established for each assay as the assay is performed but rather, a baseline can be established by referring to a form of stored information regarding a previously determined baseline level of biomarker expression for a given control sample, such as a baseline level established by any of the above-described methods. Such a form of stored information can include, for example, but is not limited to, a reference chart, listing or electronic file of population or individual data regarding “normal” (negative control) or tumor positive (including staged tumors) biomarker expression; a medical chart for the patient recording data from previous evaluations; or any other source of data regarding baseline biomarker expression that is useful for the patient to be diagnosed.

After the level of biomarker expression or biological activity is detected in the sample to be evaluated for tumor cell growth, such level is compared to the established baseline level of biomarker expression or biological activity, determined as described above. Also, as mentioned above, preferably, the method of detecting used for the sample to be evaluated is the same or qualitatively and/or quantitatively equivalent to the method of detecting used to establish the baseline level, such that the levels of the test sample and the baseline can be directly compared. In comparing the test sample to the baseline control, it is determined whether the test sample has a measurable decrease or increase in biomarker expression or biological activity over the baseline level, or whether there is no statistically significant difference between the test and baseline levels. After comparing the levels of biomarker expression or biological activity in the samples, the final step of making a diagnosis, monitoring, or staging of the patient can be performed as discussed above.

As discussed above, a positive diagnosis indicates that increased cell growth, and possibly tumor cell growth (neoplastic transformation), has occurred, is occurring, or is statistically likely to occur in the cells or tissue from which the sample was obtained. In order to establish a positive diagnosis, the level of biomarker activity is modulated as compared to the established baseline by an amount that is statistically significant (i.e., with at least a 95% confidence level, or p<0.05). Preferably, detection of at least about a 10% change in biomarker expression or biological activity in the sample as compared to the baseline level results in a positive diagnosis of cancer for said sample, as compared to the baseline. More preferably, detection of at least about a 30% change in biomarker expression or biological activity in the sample as compared to the baseline level results in a positive diagnosis of cancer for said sample, as compared to the baseline. More preferably, detection of at least about a 50% change, and more preferably at least about a 70% change, and more preferably at least about a 90% change, or any percentage change between 5% and higher in 1% increments (i.e., 5%, 6%, 7%, 8% . . . ) in biomarker expression or biological activity in the sample as compared to the baseline level results in a positive diagnosis of cancer for said sample. In one embodiment, a 1.5 fold change in biomarker expression or biological activity in the sample as compared to the baseline level results in a positive diagnosis of cancer for said sample. More preferably, detection of at least about a 3 fold change, and more preferably at least about a 6 fold change, and even more preferably, at least about a 12 fold change, and even more preferably, at least about a 24 fold change, or any fold change from 1.5 up in increments of 0.5 fold (i.e., 1.5, 2.0, 2.5, 3.0 . . . ) in biomarker expression or biological activity as compared to the baseline level, results in a positive diagnosis of cancer for said sample.

Once a positive diagnosis is made using the present method, the diagnosis can be substantiated, if desired, using any suitable alternate method of detection of tumor cells, including pathology screening, blood screening for tumor antigens, and surgery.

Included in the present invention are kits for assessing angiogenesis in cells or for diagnosing tumor cells (cancer) in a patient. The assay kit includes: (a) reagents for detecting biomarker expression or activity in a test sample (e.g., a probe that hybridizes under stringent hybridization conditions to a nucleic acid molecule encoding the biomarker or a fragment thereof; RT-PCR primers for amplification of mRNA encoding the biomarker or a fragment thereof; and/or an antibody, antigen-binding fragment thereof or other antigen-binding peptide that selectively binds to the biomarker); and (b) reagents for detecting a control marker characteristic of a cell type in the test sample (e.g., a probe that hybridizes under stringent hybridization conditions to a nucleic acid molecule encoding a protein marker; PCR primers which amplify such a nucleic acid molecule; and/or an antibody, antigen binding fragment thereof, or antigen binding peptide that selectively binds to the control marker in the sample).

The reagents for detecting of part (a) and or part (b) of the assay kit of the present invention can be conjugated to a detectable tag or detectable label. Such a tag can be any suitable tag which allows for detection of the reagents of part (a) or (b) and includes, but is not limited to, any composition or label detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Useful labels in the present invention include biotin for staining with labeled streptavidin conjugate, magnetic beads (e.g., Dynabeads™), fluorescent dyes (e.g., fluorescein, texas red, rhodamine, green fluorescent protein, and the like), radiolabels (e.g., ³H, ¹²⁵I, ³⁵S, ¹⁴C, or ³²p), enzymes (e.g., horse radish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and colorimetric labels such as colloidal gold or colored glass or plastic (e.g., polystyrene, polypropylene, latex, etc.) beads.

In addition, the reagents for detecting of part (a) and or part (b) of the assay kit of the present invention can be immobilized on a substrate. Such a substrate can include any suitable substrate for immobilization of a detection reagent such as would be used in any of the previously described methods of detection. Briefly, a substrate suitable for immobilization of a means for detecting includes any solid support, such as any solid organic, biopolymer or inorganic support that can form a bond with the means for detecting without significantly effecting the activity and/or ability of the detection means to detect the desired target molecule. Exemplary organic solid supports include polymers such as polystyrene, nylon, phenol-formaldehyde resins, acrylic copolymers (e.g., polyacrylamide), stabilized intact whole cells, and stabilized crude whole cell/membrane homogenates. Exemplary biopolymer supports include cellulose, polydextrans (e.g., Sephadex®), agarose, collagen and chitin. Exemplary inorganic supports include glass beads (porous and nonporous), stainless steel, metal oxides (e.g., porous ceramics such as ZrO₂, TiO₂, Al₂O₃, and NiO) and sand.

According to the present invention, the method and assay for assessing tumor cells in a patient, as well as other methods disclosed herein, are suitable for use in a patient that is a member of the Vertebrate class, Mammalia, including, without limitation, primates, livestock and domestic pets (e.g., a companion animal). Most typically, a patient will be a human patient.

The following examples are provided for the purpose of illustration and are not intended to limit the scope of the present invention. Each publication or other reference disclosed below and elsewhere herein is incorporated herein by reference in its entirety.

EXAMPLES

The following Materials and Methods were used in Examples 1-5 below.

Plasmids

All retroviral expression vectors encoding various putative angiogenic factors were generated by first PCR amplifying their full-length cDNAs from expressed sequence tags using oligonucleotides that facilitated their subsequent subcloning into the pcDNA3.1/Myc-His B vector (Invitrogen). The resulting full-length Myc-His₆-tagged cDNAs were PCR amplified using oligonucleotides that permitted their ligation into the bicistronic retroviral vector, pMSCV-IRES-YFP (Albig and Schiemann, 2005). Table II identifies all of the IMAGE clones and oligonucleotides used to synthesize these retroviral vectors. All putative angiogenic factor inserts were sequenced in their entirety on an Applied Biosystems 377A DNA sequencing machine. TABLE II Cloning oligonucleotides Gene Image Oligos for subcloning name clone to pcDNA3.1/Myc-His Oligos for subcloning to pMSCV-YFP Matri- 5063535 5′(NotI)GGCGGCGCGGCCGCATGGAGAAGATGTTGGTG 5′(XhoI)GGCGGCCTCGAGATGGAGAAGATGTTGGTG lin-2 SEQ ID NO:57 SEQ ID NO:59 3′(SacII)GGCGGCCCGCGGTCTGTATTTTAGGCGATT 3′(EcoRI)CCGGCCGAATTCTCAATGGTGATGGTGATGATGACC SEQ ID NO:58 SEQ ID NO:60 Lumican 5707371 5′(BamH1)GGCGCCGGATCCATGAATGTATGTGCGTTC 5′(BgIII)GGCGCCAGATCTATGAATGTATGTGCGTTC SEQ ID NO:61 SEQ ID NO:63 3′(NotI)GGCGCCGGATCCATGAATGTATGTGCGTTC 3′(EcoRI)CCGGCCGAATTCTCAATGGTGATGGTGATGATGACC SEQ ID NO:62 SEQ ID NO:64 ECM1 5347298 5′(BamHI)GGCGGCGGATCCATGGGGACCGTATCCAGA 5′(ECM1)GGCGCCAGATCTATGAATGTATGTGCGTTC SEQ ID NO:65 SEQ ID NO:67 3′(SacII)GGCGGCCCGCGGTTCTTCCTTGGACCCAGG 3′(HpaI)GGCCGGGTTAACTCAATGGTGATGGTGATGATG SEQ ID NO:66 SEQ ID NO:68 SMOC-2 3988177 5′(HindIII)GGCGGCAAGCTTATGCTGCCGCCACAGCTG 5′(BgIII)GGCGGCCTCGAGATGTGGCCCCAACCACCC SEQ ID NO:69 SEQ ID NO:71 3′(SacII)GGCGGCCCGCGGTCCTTGTTTCCTGGGCTG 3′(EcoRI)CCGGCCGAATTCTCAATGGTGATGGTGATGATGACC SEQ ID NO:70 SEQ ID NO:72 MAGP-2 3469761 5′(HindIII)GGCGGCAAGCTTATGCTGTTCTTGGGGCAG 5′(XhoI)GGCGGCCTCGAGATGTGGCCCCAACCACCC SEQ ID NO:73 SEQ ID NO:75 3′(SacII)GGCGGCCCGCGGCAGACCATCGGGTCTCTG 3′(EcoRI)CCGGCCGAATTCTCAATGGTGATGGTGATGATGACC SEQ ID NO:74 SEQ ID NO:76 AK002276 1481807 5′(HindIII)GGCGGCAAGCTTATGGCGTCTCGGGAGTCA 5′(EcoRI)GGCGGCGAATTCATGGCGTCTCGGGAGTCA SEQ ID NO:77 SEQ ID NO:79 3′(SacIII)GGCGGCCCGCGGTGAAGCCTTGGCTTTCCG 3′(EcoRI)CCGGCCGAATTCTCAATGGTGATGGTGATGATGACC SEQ ID NO:78 SEQ ID NO:80 CRELD-2 6336331 5′(HindIII)GGCGGCCCGCGGTGAAGCCTTGGCTTTCCG 5′(BgIII)GGCGGCAGATCTATGCACCTGCTGCTTGCA SEQ ID NO:81 SEQ ID NO:83 3′(SacII)GGCGGCCCGCGGCAAATCCTCACGGGAGGG 3′(XhoI)CCGGCCCTCGAGTCAATGGTGATGGTGATGATGACC SEQ ID NO:82 SEQ ID NO:84

The Myc-tagged mammalian expression vectors encoding murine Notch1 [pCS2+mN1FL6MT; (Mumm et al, 2000)] and Jagged-1 [pCS2+Jag1-6MT; (Mumm et al, 2000)] were kindly provided by Dr. Raphael Kopan (Washington University, St. Louis, Mo.). A retroviral Notch1 ICD vector was constructed by PCR amplifying the murine Notch1 ICD domain (amino acids 1744-2531 and contained in pCS2-mN1FL6MT) using a 5′ oligonucleotide that contained a unique Xho I restriction site, a Kozak consensus sequence, and a start codon: (5′GGCGGCCTCGAGGCCACCATGGTGCTGCTGTCCCGC; SEQ ID NO:121)

and a 3′oligonucleotide that contained a unique Hpa I restriction site, a stop codon, and the C-terminal Myc-tag: (5′GGCGGCGTTAACTCATGAATTCAAGTCCTCTTCAGA; SEQ ID NO:122) The resulting PCR product was ligated into identical restriction sites in the bicistronic retroviral vector, pMSCV-IRES-GFP (Albig and Schiemann, 2005). The pHes1-luciferase, pCMV-Hes1, and pCMV-NICD plasmids were kindly provided by Dr. Jan Jensen (University of Colorado Health Science Center, Denver, Colo.). Cell Culture and Retroviral Infections

Retroviral supernatants were produced by EcoPack2 retroviral packaging cells (Clontech, Mountain View, Calif.) and used to infect MB114 cells as described previously (Albig et al, 2006; Albig and Schiemann, 2004). Infected cells were analyzed 48 h post-infection and the highest 10% of GFP-expressing cells were collected on a MoFlo cell sorter (Cytomation, Fort Collins, Colo.). Afterward, isolated cells were expanded to yield stable polyclonal populations that were ≧95% positive for transgene expression. Human kidney 293T cells were cultured in DMEM media supplemented with 10% fetal bovine serum (FBS), while human umbilical vein ECs (HUVEC; passages 3-6) were maintained in EGM-2 media (Cambrex Corp., East Rutherford, N.J.) supplemented with EC growth factors (Bullet Kit, Cambrex).

Recombinant MAGP-2 Protein Production

A bacterial MAGP-2 expression vector was synthesized by PCR amplifying the full-length MAGP-2 cDNA (less its signal sequence) using oligonucleotides that incorporated unique Nde I (N-terminus) and Bam HI (C-terminus). The resulting PCR fragment was ligated into identical sites in pSBET (Schenk et al, 1995), which appended a FLAG-tag to the C-terminus of MAGP-2. FLAG-tagged recombinant MAGP-2 protein was purified by passing TBS/0.1% Triton X-100-solubilized bacterial cell extracts over a column containing immobilized FLAG-M2 monoclonal antibodies (Sigma, St. Louis, Mo.). Bound proteins were washed initially with 10 column volumes of TBS/0.1% Triton X-100, followed by an additional 20 column volumes of TBS. Afterward, recombinant MAGP-2 was eluted by addition of 2.5 column volumes of FLAG M2 peptide (100 □g/ml), and subsequently was concentrated by centrifugation against PBS (5 kDa cutoff; Sartorius, Goettingen, Germany).

EC Activity Assays

The effect putative angiogenic agents had on MB114 cell activities were determined as follows: (i) cell proliferation using a [³H]thymidine incorporation assay as described (Albig et al, 2006; Albig and Schiemann, 2004; Albig and Schiemann, 2005); (ii) cell invasion through Matrigel matrices using a modified Boyden-chamber assay as described (Albig et al, 2006; Albig and Schiemann, 2004; Albig and Schiemann, 2005); (iii) p38 MAPK phosphorylation using immunoblot analyses as described (Albig et al, 2006; Albig and Schiemann, 2004; Albig and Schiemann, 2005); (iv) angiogenic sprouting in rat tail collagen matrices as described (Albig et al, 2006; Albig and Schiemann, 2004); and (v) Hes1- and SBE-driven luciferase reporter gene assays as described (Albig et al, 2006; Albig and Schiemann, 2004; Albig and Schiemann, 2005).

Notch1 Processing Assay

To monitor the effects of MAGP-2 on the processing and S3 cleavage of Notch1, human kidney 293T cells were transiently transfected in 6-well plates with LT-1 liposomes containing 0.5 μg/well of Notch1 (pCS2+mN1FL6MT), 0.5 μg/well Jagged-1 (pCS2+Jag1-6MT), or 1.5 μg/well of MAGP-2 (pcDNA3.1-MAGP-2/Myc-His) in all combinations. Forty-eight h post-transfection, the cells were washed with ice-cold PBS, lysed immediately in Buffer H/1% Triton X-100 [500 μl/well; (Schiemann et al, 2002)], and incubated on ice for 30 min. Afterward, insoluble material was removed by microcentrifugation and 100 μl of the resulting clarified extract was fractionated through 6% SDS-PAGE gels. The fractionated proteins were transferred electrophoretically to nitrocellulose and probed with anti-Myc 9E10 monoclonal antibodies (Covance, Princeton, N.J.) to visual Notchi cleavage species.

Matrigel Plug Implantation Assay

The effect of MAGP-2 on vessel formation and infiltration into Matrigel plugs implanted into genetically normal mice was determined as described (Albig et al, 2006). Briefly, phenol red-free Matrigel (BD biosciences, Bedford, Mass.) was mixed with PBS (diluent), bFGF (50 or 300 ng/ml; R&D Systems, Minneapolis, Minn.), or recombinant MAGP-2 (1 μg/ml) together with bFGF (50 ng/ml), and the resulting mixtures were injected twice subcutaneously in the ventral groin area (400 μl/injection) of C57BL/6 mice. The mice were sacrificed 10 days post-implantation and the Matrigel plugs were dissected, fixed overnight in 10% formalin, and sectioned in the National Jewish Histology Laboratory. Afterward, Masson's trichrome staining was performed to visualize infiltrating vessels, which were quantified under a light microscope by determining the average number of vessels present in 5 random fields (200× magnification). Only those fields that contained at least one vessel in the area underlying the skin were tallied. Two mice were used per experimental condition and this experiment was performed three times in its entirety. All animal studies were performed according to protocol procedures approved by the Animal Care and Use Committee at National Jewish Medical and Research Center.

Semi-Quantitative Real-Time PCR

Semi-quantitative real-time PCR was performed as previously described (Albig et al, 2006; Albig and Schiemann, 2005). Briefly, MB114 cells were induced to tubulate on Matrigel matrices for 1-25 h, whereupon total RNA was isolated using the RNAqueous kit, followed by an additional round of phenol/chloroform extraction and ethanol precipitation as described above. Total RNA (1 μg) was reverse transcribed with random hexamers and iScript reverse transcriptase according to the manufacturer's recommendations (BioRad, Hercules, Calif.). The resulting cDNA reaction mixtures were diluted 40-fold in H₂O and employed in semi-quantitative real-time PCR reactions (25 μl) that used the SYBR Green PCR system (Applied Biosystems, Foster City, Calif.) supplemented with 10 μl of diluted cDNA and 0.1 μM of the oligonucleotide pairs listed in Table III. PCR reactions were performed and analyzed on an ABI 7000 sequence detection system (Applied Biosystems). Differences in RNA concentrations were controlled by normalizing individual gene signals to their corresponding GAPDH RNA signals. TABLE III Real-Time PCR oligonucleotides Real Time PCR Real-Time PCR Gene name Forward Oligonucleotide Reverse Oligonucleotide ADAMts1 5′ AATGTTTGATGGACAAGCCCC 5′ TGCTTGGATTCCTCTCCGAA SEQ ID NO:85 SEQ ID NO:86 ADAMts7 5′ ACCAGGAACGCCTACCTTTTC 5′ TCCAGTTTCCTACTTGCCAGC SEQ ID NO:87 SEQ ID NO:88 CTGF 5′ CTGCCAGTGGAGTTCAAATGC 5′ TCATTGTCCCCAGGACAGTTG SEQ ID NO:89 SEQ ID NO:90 Decorin 5′ GGCATTCAAACCTCTCGTGAA 5′ TCATGGACACGAAGTTCCTGG SEQ ID NO:91 SEQ ID NO:92 ECM1 5′ CGGAGGAATTCGTGGAAAGA 5′ CCACTAAAGCCACGTTCCTCA SEQ ID NO:93 SEQ ID NO:94 Inhibin β-a 5′ TCCCCAAGGCTAACAGAACCA 5′ CCCCTTTAAGCCCATTTCCTC SEQ ID NO:95 SEQ ID NO:96 Inhibin β-b 5′ CAGACATCGCATCCGCAAA 5′ AATGATCCAGTCGTTCCAGCC SEQ ID NO:97 SEQ ID NO:98 Integrin α-3 5′ AACCCCTTCAAACGGAACCA 5′ TCGACGTGGACAGCTGAAGAA SEQ ID NO:99 SEQ ID NO:100 Integrin α-6 5′ CTCGTTCTTCGTTCCAGGTTG 5′ AGCAGCAGCGGTGACATCTAT SEQ ID NO:101 SEQ ID NO:102 Lipocalin-7 5′ GGACAACTGCAATCGATGCA 5′ GCCTCGGTTGATGGCTTTAAT SEQ ID NO:103 SEQ ID NO:104 LoxI-3 5′ AAGTGTGACAGAATGCGCCTC 5′ ACTTGCAACTGATGCTCCACC SEQ ID NO:105 SEQ ID NO:106 Lumican 5′ AGTGTGCCAATGGTTCCTCCT 5′ TGCAGGTCTGTGACGTTCTCA SEQ ID NO:107 SEQ ID NO:108 Matrilin-2 5′ CACAGGCATCCTGATCTTTGC 5′ TGAAATTGGCCACCAGGAAG SEQ ID NO:109 SEQ ID NO:110 Nephronectin 5′ GGTGATGGAGGACATGCGAAT 5′ TTGTTGGCTTGGAAGTAGGCC SEQ ID NO:111 SEQ ID NO:112 SerpinE-2 5′ AATCTGATCGATGGTGCCCTT 5′ CGAATGTCCGTTTCTTTGTGC SEQ ID NO:113 SEQ ID NO:114 SMOC-2 5′ CACCAAATGGAAGACCCATCA 5′ ATCATCTGCTTTCCCTGCTCC SEQ ID NO:115 SEQ ID NO:116 CRELD-2 5′ GCAGAGGAACGAGACCCACAGCATC 5′ GTGCCCAGCCCACTTCACACTG SEQ ID NO:117 SEQ ID NO:118 MAGP-2 5′ GCTTGTCTTGGCAGTCAGCATCCC 5′ GGTCGTCTGTGAATGTCTCAGGCAC SEQ ID NO:119 SEQ ID NO:120 Oligonucleotide Microarray Analysis

Murine brain microvascular MB114 ECs were cultured as previously described (Albig et al, 2006; Albig and Schiemann, 2004). To identify genes differentially expressed during angiogenesis, log phase-growing MB114 cells (2×10⁶ cells/plate) were plated onto 10-cm plates that contained 4 ml of solidified Matrigel matrices [diluted 5:3 in serum-free media (SFM)]. Tubulogenesis was allowed to proceed for 1, 5, 15, or 25 h, at which point the cells were gently washed twice with ice-cold PBS, and subsequently were scraped, together with their Matrigel cushions, into 16 ml of lysis/binding buffer to isolate total RNA using the RNAqueous kit (Ambion, Austin, Tex.). Isolated total RNA samples were subjected to phenol:choloroform extraction and ethanol precipitation, followed by additional purification using the RNeasy kit (Qiagen, Valencia, Calif.). Afterward, the quality and integrity of purified total RNA (1.5 μg/lane) was analyzed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, Calif.). Biotin-labeled cRNA probes were synthesized using 8 μg of total RNA that was primed with olido-dT and reverse transcribed with Superscript II (Invitrogen, Carlsbad, Calif.), and subsequently were fragmented and hybridized overnight to Affymetrix MOE430A GeneChips according to the manufacturer's recommendations (Affymetrix, Santa Clara, Calif.) in the University of Colorado Health Sciences Center Microarray Core Facility. The microarrays were scanned (2.5-3μ resolution) on a Affymetrix GeneChip Scanner 3000, and differentially expressed mRNAs were identified using GeneSpring 6.0 software (Agilent Technologies). In doing so, individual time points were first compiled into a single experiment that was filtered on flags (i.e., 6 out of 12 flags needed to pass filter). The remaining genes then were filtered by expression levels such that only those genes that were differentially regulated ≧3-fold≦ in at least one time point were considered significant.

Example 1

The following example describes the identification of secretory proteins differentially expressed in tubulating ECs.

To characterize the secretome of ECs undergoing tumor-induced angiogenesis, murine brain microvascular MB114 cells were cultured on tumor-derived basement membranes (i.e., Matrigel matrices) to stimulate angiogenesis activation and the formation of capillary-like structures in vitro. MB114 cells cultured onto Matrigel matrices for 0-25 hours as indicated in FIG. 6 spontaneously reorganized into elongated, capillary-like structures, a response that was readily detected by 5 h, and one that continued to develop over the next 20 h (FIG. 6). Total RNA was isolated at various times after the initiation of tubulogenesis in MB114 cells, and subsequently was used to synthesize biotinylated cRNA probes that were hybridized to Affymetrix MOE430 GeneChips (see Materials and Methods). In doing so, 308 genes were identified whose expression in angiogenic ECs was altered ≧3-fold≦. Of these differentially-expressed genes, 63 genes (˜20%) encoded EC secretory proteins (Table I), 35 genes (˜11%) encoded transmembrane or membrane-associated proteins (Table V), and 210 genes encoded non-secretory proteins (Table IV). This approach identified several secretory proteins known to be associated with angiogenesis and/or microenvironment remodeling, including ADAMTS1 (Iruela-Arispe et al, 2003), CTGF (Brigstock, 2002), HGF (Gao and Vande Woude, 2005), MMPs 3 and 9 (Heissig et al, 2003), thrombospondins 1 and 2 (Armstrong and Bornstein, 2003), and TIMP3 (Qi et al, 2003) (Table I, bold type face). In addition, numerous secretory proteins not previously associated with angiogenesis were identified (Table I, regular text face). The differential expression of 19 individual genes was verified by semi-quantitative real-time PCR (see Materials and Methods). These analyses showed significant concordance in the expression profiles measured either by real-time PCR or microarray analyses (Table VI), indicating that these (and other) genes are indeed bona fide targets of angiogenic. signaling systems in tubulating ECs. TABLE I Secreted proteins differentially regulated during MB114 tubulogenesis. Hours of tubulogenesis Name GenBank # 1 5 15 25 Description 9130213B05Rik BC006604 1.0 0.3 0.3 0.6 RIKEN cDNA 9130213B05 gene (has signal peptide) Adamts1 D67076 1.0 0.3 0.6 0.8 Adamts1 Adamts7 AL359935 1.0 2.4 4.8 4.2 Adamts7 C1r NM_023143 1.0 1.0 2.3 5.6 complement component 1, r subcomponent C1s BC022123 1.0 1.0 3.8 10.7 complement component 1, s subcomponent C3 K02782 1.0 0.7 7.9 23.0 complement component 3 Ccl2 AF065933 1.0 0.7 0.2 0.1 chemokine (C-C motif) ligand 2 Ccl5 NM_013653 1.0 2.7 3.4 3.2 chemokine (C-C motif) ligand 5 Ccl7 AF128193 1.0 0.5 0.3 0.3 chemokine (C-C motif) ligand 7 Ccl8 NM_021443 1.0 1.1 2.8 4.9 chemokine (C-C motif) ligand 8 Cfh AI987976 1 1.5 3.4 12.5 complement component factor h Clu NM_013492 1.0 0.9 1.7 6.6 clusterin Col3a1 AW550625 1.0 1.3 3.0 3.9 procollagen, type III, alpha 1 Col9a3 BG074456 1.0 0.8 6.7 3.2 procollagen, type IX, alpha 3 Creld2 AK017880 1.0 3.1 1.0 1.1 cysteine-rich with EGF-like domains 2 Csf3 NM_009971 1.0 1.7 0.3 0.3 colony stimulating factor 3 (granulocyte) Ctgf NM_010217 1.0 0.2 0.3 0.3 connective tissue growth factor Cxcl16 BC019961 1 3.9 3.4 3.0 chemokine (C-X-C motif) ligand 16 Cxcl2 NM_009140 1.0 1.2 0.2 0.1 chemokine (C-X-C motif) ligand 2 Cyr61 NM_010516 1.0 0.5 0.3 0.2 cysteine rich protein 61 Dcn NM_007833 1.0 2.1 6.9 11.0 decorin Ecm1 NM_007899 1.0 1.7 2.9 3.6 extracellular matrix protein 1 F3 BC024886 1.0 0.2 0.2 0.4 coagulation factor III Grem1 BC015293 1.0 3.8 2.5 3.9 cysteine knot superfamily 1, BMP antagonist 1 Hgf AF042856 1.0 1.2 4.4 5.0 hepatocyte growth factor Igfbp4 BC019836 1.0 1.7 3.5 4.3 insulin-like growth factor binding protein 4 Igfbp5 NM_010518 1.0 0.9 3.8 5.2 insulin-like growth factor binding protein 5 Il6 NM_031168 1.0 3.1 3.2 2.7 interleukin 6 Inhba NM_008380 1.0 1.9 0.4 0.3 inhibin beta-A Lbp NM_008489 1.0 0.7 2.3 5.2 lipopolysaccharide binding protein Lcn2 X14607 1.0 1.3 24.7 97.3 lipocalin 2 Lcn7 BC005738 1.0 0.6 0.3 0.3 lipocalin 7 Lif AF065917 1.0 0.6 0.2 0.1 leukemia inhibitory factor Loxl3 NM_013586 1.0 1.2 4.0 4.7 lysyl oxidase-like 3 Lum AK014312 1.0 1.1 1.8 3.2 lumican MFAP5 (MAGP-2) NM_015776 1.0 3.2 1.0 1.2 microfibrillar associated protein 5 Matn2 BC005429 1.0 1.4 6.4 9.9 Matrilin-2 matrix gamma- Mglap NM_008597 1.0 1.9 7.4 17.8 carboxyglutamate (gla) protein Mmp10 NM_019471 1.0 5.4 11.8 12.1 matrix metalloproteinase 10 Mmp11 NM_008606 1.0 1.4 4.9 9.4 matrix metalloproteinase 11 Mmp19 AF153199 1.0 1.9 5.7 9.4 matrix metalloproteinase 19 Mmp3 NM_010809 1.0 1.6 3.5 10.3 matrix metalloproteinase 3 Mmp9 NM_013599 1.0 4.4 5.7 3.6 matrix metalloproteinase 9 Naga BC021631 1.0 1.6 4.4 8.2 N-acetyl galactosaminidase, alpha Nbl1 NM_008675 1.0 1.2 2.8 5.8 neuroblastoma, suppression of tumorigenicity 1 Ngfb NM_013609 1.0 0.3 0.1 0.1 nerve growth factor, beta Npnt AA223007 1 0.6 0.2 0.2 Nephronectin Npr3 NM_008728 1.0 0.6 0.2 0.2 natriuretic peptide receptor 3 Olfm1 D78264 1.0 1.5 3.6 3.2 olfactomedin 1 Plau NM_008873 1.0 0.9 0.2 0.3 plasminogen activator, urokinase Ptx3 NM_008987 1.0 0.1 0.3 0.3 pentaxin related gene serine (or cysteine) Serpinb2 NM_011111 1.0 1.8 1.4 1.9 proteinase inhibitor, clade B, member 2 serine (or cysteine) Serpine1 NM_008871 1.0 0.6 0.2 0.1 proteinase inhibitor, clade E, member 1 Serpine2 NM_009255 1.0 3.6 16.3 29.5 serine (or cysteine) proteinase inhibitor, clade E, member 2 Sfrp2 NM_009144 1.0 0.8 4.1 5.5 secreted frizzled-related sequence protein 2 Slpi NM_011414 1.0 1.2 3.7 6.9 secretory leukocyte protease inhibitor Smoc2 NM_022315 1.0 7.2 10.6 5.5 Secreted modular calcium binding protein-2 Tgfb3 BC014690 1.0 5.4 2.2 2.8 transforming growth factor, beta 3 Thbs1 AI385532 1.0 0.2 0.4 0.5 thrombospondin 1 Thbs2 NM_011581 1.0 0.9 3.6 6.6 thrombospondin 2 Timp3 BI111620 1.0 0.6 0.2 0.1 tissue inhibitor of metalloproteinase 3 U90926 NM_020562 1.0 1.0 0.3 0.3 cDNA sequence U90926 (predicted signal peptide) Wisp1 NM_018865 1.0 0.9 0.4 0.2 WNT1 inducible signaling pathway protein 1

Shown in Table I are differentially-expressed genes that encode for secretory proteins whose expression was altered at least 3-fold in at least one time point during the angiogenic timecourse. in tubulating ECs. Identified genes encoding known angiogenic regulators are shown in bold type face. Identified genes encoding putative angiogenic regulators are shown in regular text face. TABLE IV Non-secretory proteins differentially regulated during MB114 tubulogenesis Hours of Tubulogenesis Name GenBank # 1 5 15 25 Description Abca1 BB144704 1.0 1.6 4.8 5.4 ATP-binding cassette, sub-family A (ABC1), member 1 Abca7 NM_013850 1.0 1.2 3.4 4.1 ATP-binding cassette, sub-family A (ABC1), member 7 Abcb1a M30697 1.0 3.6 4.1 2.7 ATP-binding cassette, sub-family B (MDR/TAP), member 1A Abhd4 NM_134076 1.0 1.1 3.4 3.8 abhydrolase domain containing 4 Abtb1 NM_030251 1.0 1.9 5.0 5.4 ankyrin repeat and BTB (POZ) domain containing 1 Acta2 NM_007392 1.0 0.7 0.2 0.2 actin, alpha 2, smooth muscle, aorta Actg2 NM_009610 1.0 0.7 0.3 0.3 actin, gamma 2, smooth muscle, enteric Ahi1 BQ175532 1.0 3.2 3.4 2.5 Abelson helper integration site Akr1c18 NM_134066 1.0 1.9 6.1 9.1 aldo-keto reductase family 1, member C18 Ampd3 D85596 1.0 1.0 3.7 3.7 AMP deaminase 3 Ankrd1 AK009959 1.0 0.3 0.3 0.2 ankyrin repeat domain 1 (cardiac muscle) Aox1 NM_009676 1.0 1.0 6.7 11.8 aldehyde oxidase 1 Apbb3 BC024809 1.0 2.0 4.2 6.1 amyloid beta (A4) precursor protein-binding, family B, member 3 Aps NM_018825 1.0 2.5 4.1 3.5 adaptor protein with pleckstrin homology and src Arc NM_018790 1.0 0.3 0.2 0.1 activity regulated cytoskeletal-associated protein Arg2 NM_009705 1.0 1.4 4.1 5.2 arginase type II Ass1 NM_007494 1.0 1.7 3.0 3.7 argininosuccinate synthetase 1 Bckdha NM_007533 1.0 1.6 3.3 3.3 branched chain ketoacid dehydrogenase E1, alpha polypeptide Atoh8 AK016909 1.0 8.5 9.3 6.8 atonal homolog 8 (Drosophila) Bbs2 AF342737 1.0 1.8 3.6 4.2 Bardet-Biedl syndrome 2 homolog (human) Bhlhb2 NM_011498 1.0 0.3 0.2 0.3 basic helix-loop-helix domain containing, class B2 Bst1 AI647987 1.0 1.4 3.9 5.9 bone marrow stromal cell antigen 1 Cbfa2t1h X79989 1.0 0.4 4.7 8.4 CBFA2T1 identified gene homolog (human) Cbr2 BC010758 1.0 1.1 5.3 18.0 carbonyl reductase 2 Ccnb1 AU015121 1.0 0.9 0.3 0.2 cyclin B1 Ccng2 U95826 1.0 1.7 3.4 3.1 cyclin G2 Cdc6 NM_011799 1.0 0.7 0.2 0.1 cell division cycle 6 homolog (S. cerevisiae) Cdk5r BB177836 1.0 0.5 0.2 0.2 cyclin-dependent kinase 5, regulatory subunit (p35) Cdkn1a AK007630 1.0 1.9 0.2 0.1 cyclin-dependent kinase inhibitor 1A (P21) Cebpd BB831146 1.0 3.6 6.5 8.8 CCAAT/enhancer binding protein (C/EBP), delta Chc1 NM_133878 1.0 1.0 0.3 0.2 chromosome condensation 1 Cit AF086823 1.0 4.0 3.5 0.5 citron Cte1 NM_012006 1.0 1.0 5.0 7.1 mitochondrial acyl-CoA thioesterase 1 Cyp51 NM_020010 1.0 0.5 0.2 0.3 cytochrome P450, 51 Cyp7b1 NM_007825 1.0 3.5 3.9 6.6 cytochrome P450, family 7, subfamily b, polypeptide 1 Dbp BB550183 1.0 0.6 5.1 7.7 D site albumin promoter binding protein Dck BB030204 1.0 1.0 0.3 0.1 deoxycytidine kinase Dcxr BC012247 1.0 2.3 8.4 20.7 dicarbonyl L-xylulose reductase Dhrs7 AK009385 1.0 1.8 3.5 5.6 dehydrogenase/reductase (SDR family) member 7 Dhrs8 NM_053262 1.0 0.9 4.8 5.4 dehydrogenase/reductase (SDR family) member 8 Diap3 NM_019670 1.0 0.5 0.2 0.1 diaphanous homolog 3 (Drosophila) Dio2 AF177196 1.0 0.5 5.5 25.1 deiodinase, iodothyronine, type II Dscr1 AF282255 1.0 0.5 0.2 0.2 Down syndrome critical region homolog 1 (human) Dusp2 L11330 1.0 0.3 0.2 0.1 dual specificity phosphatase 2 Dusp9 AV295798 1.0 1.0 0.2 0.1 dual specificity phosphatase 9 Ech1 NM_016772 1.0 1.5 3.1 4.9 enoyl coenzyme A hydratase 1, peroxisomal Egr1 NM_007913 1.0 0.2 0.3 0.3 early growth response 1 Egr2 X06746 1.0 0.2 0.2 0.2 early growth response 2 Erdr1 AJ007909 1.0 0.6 0.3 0.3 DNA segment, Chr 14, Wayne State University 89, expressed Fabp5 BC002008 1.0 1.0 0.3 0.2 fatty acid binding protein 5, epidermal Fbxo32 AF441120 1.0 1.4 9.3 16.4 F-box only protein 32 Fos AV026617 1.0 0.2 0.2 0.3 FBJ osteosarcoma oncogene Fosl1 U34245 1.0 0.8 0.2 0.2 fos-like antigen 1 Foxm1 NM_008021 1.0 0.6 0.3 0.0 forkhead box M1 Gabpb1 NM_010249 1.0 0.9 0.2 0.2 GA repeat binding protein, beta 1 Ggtl3 BC005772 1.0 2.4 3.3 4.1 gamma-glutamyltransferase-like 3 Gjb3 NM_008126 1.0 0.9 0.2 0.2 gap junction membrane channel protein beta 3 Gstt3 BC003903 1.0 1.3 3.7 3.6 glutathione S-transferase, theta 3 Hbp1 BC026853 1.0 1.1 3.0 3.5 high mobility group box transcription factor 1 Hdac11 BC016208 1.0 0.7 4.2 5.9 histone deacetylase 11 Hmgcr BB123978 1.0 0.5 0.3 0.3 3-hydroxy-3-methylglutaryl-Coenzyme A reductase Hmgcs1 BB705380 1.0 0.3 0.3 0.4 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 Hnrpab NM_010448 1.0 0.8 0.3 0.3 heterogeneous nuclear ribonucleoprotein A/B Hs6st2 AW536432 1.0 0.5 0.3 0.3 heparan sulfate 6-O-sulfotransferase 2 Hsd17b7 NM_010476 1.0 0.4 0.2 0.3 hydroxysteroid (17-beta) dehydrogenase 7 Idi1 BC004801 1.0 0.5 0.2 0.3 isopentenyl-diphosphate delta isomerase Ier2 NM_010499 1.0 0.5 0.3 0.3 immediate early response 2 Ier5 BF147705 1.0 0.5 0.3 0.3 immediate early response 5 Ifi203 M74124 1.0 8.5 8.4 7.2 interferon activated gene 205 Ifrd1 NM_013562 1.0 0.4 0.2 0.2 interferon-related developmental regulator 1 Junb NM_008416 1.0 0.4 0.3 0.3 Jun-B oncogene Kcnip1 NM_027398 1.0 0.8 0.2 0.1 Kv channel-interacting protein 1 Klf4 BG069413 1.0 0.5 0.2 0.2 Kruppel-like factor 4 (gut) Kpnb1 NM_008379 1.0 0.6 0.3 0.3 karyopherin (importin) beta 1 Lhx1 AV335209 1.0 0.4 0.2 0.2 LIM homeobox protein 1 Lyar NM_025281 1.0 1.0 0.3 0.2 Ly1 antibody reactive clone Mafk NM_010757 1.0 0.3 0.3 0.3 v-maf musculoaponeurotic fibrosarcoma oncogene family, protein K (avian) Map3k5 NM_008580 1.0 3.4 4.2 4.2 mitogen activated protein kinase kinase kinase 5 Mark1 BM213279 1.0 1.7 8.6 18.7 MAP/microtubule affinity-regulating kinase 1 Mcm3 B1658327 1.0 0.8 0.3 0.1 minichromosome maintenance deficient 3 (S. cerevisiae) Mgst2 AV066880 1.0 2.3 11.2 17.9 microsomal glutathione S-transferase 2 Mthfd2 BG076333 1.0 1.4 0.2 0.2 methylenetetrahydrofolate dehydrogenase (NAD+ dependent), methenyltetrahydrofolate cyclohydrolase Mybl2 NM_008652 1.0 0.9 0.3 0.2 myeloblastosis oncogene-like 2 Myd116 NM_008654 1.0 0.4 0.3 0.3 myeloid differentiation primary response gene 116 Myl9 AK007972 1.0 0.6 0.1 0.3 myosin, light polypeptide 9, regulatory Narg2 BE952805 1.0 4.1 3.7 2.8 NMDA receptor-regulated gene 2 Ndrg2 NM_013864 1.0 1.5 5.0 5.1 N-myc downstream regulated 2 Ndrg4 AV006122 1.0 1.5 3.8 3.4 N-myc downstream regulated 4 Nfatc4 BF227641 1.0 0.9 4.4 5.1 nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4 Nfkbia NM_010907 1.0 0.5 0.3 0.3 nuclear factor of kappa light chain gene enhancer in B- cells inhibitor, alpha Nolc1 BM213850 1.0 0.8 0.3 0.2 nucleolar and coiled-body phosphoprotein 1 Nr4a2 NM_013613 1.0 1.7 4.3 4.1 nuclear receptor subfamily 4, group A, member 2 Nudt7 AK011172 1.0 2.2 3.1 4.1 nudix (nucleoside diphosphate linked moiety X)-type motif 7 Pa2g4 AA672939 1.0 0.8 0.3 0.2 proliferation-associated 2G4 Parc BC026469 1.0 1.4 3.4 3.6 p53-associated parkin-like cytoplasmic protein Paxip1 AW742928 1.0 0.8 0.3 0.3 PAX interacting (with transcription-activation domain) protein 1 Pdk2 NM_133667 1.0 0.9 3.7 4.6 pyruvate dehydrogenase kinase, isoenzyme 2 Pdzrn3 NM_018884 1.0 0.7 3.1 5.1 semaF cytoplasmic domain associated protein 3 Phyh NM_010726 1.0 1.3 3.5 5.6 phytanoyl-CoA hydroxylase Plk4 AI385771 1.0 0.7 0.3 0.1 polo-like kinase 4 (Drosophila) Pprc1 BM199989 1.0 0.6 0.3 0.2 cDNA sequence BC013720 Ptp4a1 BC003761 1.0 0.4 0.3 0.3 protein tyrosine phosphatase 4a1 Ptpre U35368 1.0 1.0 0.3 0.3 protein tyrosine phosphatase, receptor type, E Ran AV090150 1.0 0.9 0.3 0.2 RAN, member RAS oncogene family Rgs16 U94828 1.0 1.3 0.2 0.2 regulator of G-protein signaling 16 Rgs2 AF215668 1.0 2.4 7.9 12.4 regulator of G-protein signaling 2 Rgs5 NM_133736 1.0 2.0 4.8 6.5 regulator of G-protein signaling 5 Rin2 AK014548 1.0 2.1 3.4 4.5 Ras and Rab interactor 2 Rnase4 BC005569 1.0 1.0 5.0 9.2 RIKEN cDNA C730049F20 gene Rps10 AV283093 1.0 0.7 0.3 0.3 RIKEN cDNA 2210402A09 gene Sc4mol AK005441 1.0 0.6 0.2 0.2 sterol-C4-methyl oxidase-like Sdpr BE197945 1.0 0.2 0.2 0.2 serum deprivation response Sesn1 AV016566 1.0 1.2 3.3 3.4 sestrin 1 Shmt1 AF237702 1.0 1.0 0.3 0.1 serine hydroxymethyl transferase 1 (soluble) Sil BC004585 1.0 0.7 0.3 0.2 Tal1 interrupting locus Snrpa1 BC013777 1.0 0.9 0.3 0.2 small nuclear ribonucleoprotein polypeptide A′ Socs3 BB241535 1.0 2.1 4.3 6.3 suppressor of cytokine signaling 3 Sox9 BC024958 1.0 0.4 0.3 0.3 SRY-box containing gene 9 Srm NM_009272 1.0 0.9 0.3 0.3 spermidine synthase T2bp BB277065 1.0 1.2 4.9 7.1 Traf2 binding protein Tagln BB114067 1.0 0.9 0.2 0.1 transgelin Tcofl AW209012 1.0 0.8 0.3 0.2 Treacher Collins Franceschetti syndrome 1, homolog Timm8a W82151 1.0 1.1 0.2 0.2 translocase of inner mitochondrial membrane 8 homolog a (yeast) Tiparp BB707122 1.0 0.3 0.2 0.2 TCDD-inducible poly(ADP-ribose)polymerase Tle2 AU067681 1.0 0.9 4.2 8.0 transducin-like enhancer of split 2, homolog of Drosophila E(spl) Tle6 NM_053254 1.0 1.1 3.2 3.5 transducin-like enhancer of split 6, homolog of Drosophila E(spl) Tnfaip3 NM_009397 1.0 0.4 0.1 0.1 tumor necrosis factor, alpha-induced protein 3 Tnnt2 NM_011619 1.0 10.6 9.1 1.4 troponin T2, cardiac Tprt AK011869 1.0 0.8 0.3 0.2 trans-prenyltransferase Trib1 AV237242 1.0 0.5 0.2 0.3 tribbles homolog 1 (Drosophila) Trip13 AK010336 1.0 1.0 0.3 0.1 thyroid hormone receptor interactor 13 Txnip AF173681 1.0 2.8 4.3 4.9 thioredoxin interacting protein Ugt1a2 BC019434 1.0 2.4 4.2 6.5 UDP glycosyltransferase 1 family, polypeptide A6 Uhrfl BB702754 1.0 0.7 0.3 0.1 ubiquitin-like, containing PHD and RING finger domains, 1 Ung BC004037 1.0 0.5 0.2 0.2 uracil-DNA glycosylase Xdh AV286265 1.0 1.1 9.2 27.5 xanthine dehydrogenase Zfp36 X14678 1.0 0.3 0.3 0.3 TIS11 (AA 1-183); Mouse TPA-induced TIS11 mRNA. Zfp36l2 BG094962 1.0 0.3 0.4 0.3 zinc finger protein 36, C3H type-like 2 Zfp60 NM_009560 1.0 4.5 6.2 4.2 zinc finger protein 60 ESTs Hours of Tubulogenesis Name GenBank # 1 5 15 25 AA223007 1.0 0.6 0.2 0.2 AA414485 1.0 0.7 0.3 0.3 AA672926 1.0 0.5 0.3 0.2 AI324124 1.0 0.3 0.2 0.2 AK009010 1.0 0.6 0.2 0.2 AK011311 1.0 1.2 0.3 0.2 AK012043 1.0 0.6 0.3 0.3 AK014587 1.0 0.4 0.3 0.2 AK015966 1.0 0.7 0.3 0.3 AK017688 1.0 2.5 5.9 3.8 AK018202 1.0 1.7 3.4 3.6 AU017197 1.0 0.7 0.3 0.1 AU018569 1.0 1.0 0.3 0.2 AV167760 1.0 0.5 0.3 0.3 AV171622 1.0 1.6 3.5 5.3 AV171622 1.0 1.6 4.6 6.1 AV171622 1.0 1.5 4.6 7.7 AV209892 1.0 1.9 3.6 4.3 AV221013 1.0 0.7 0.3 0.3 AV232798 1.0 0.5 0.2 0.3 AV371987 1.0 1.9 3.8 6.3 AV374246 1.0 0.5 0.3 0.3 AW488471 1.0 0.8 0.2 0.2 AW554921 1.0 1.1 0.2 0.0 AW744519 1.0 5.6 14.8 18.5 AW744519 1.0 2.1 5.5 6.0 AY029778 1.0 1.1 16.1 24.5 BB010153 1.0 1.9 3.1 4.2 BB042892 1.0 0.3 0.3 0.1 BB230053 1.0 1.0 0.2 0.2 BB332449 1.0 1.1 5.8 9.7 BB371300 1.0 3.9 4.5 5.1 BB377340 1.0 1.2 3.3 4.8 BB407228 1.0 0.7 0.3 0.3 BB530223 1.0 1.3 5.0 4.7 BB550907 1.0 0.5 9.1 32.0 BB628049 1.0 1.3 3.2 3.5 BC006604 1.0 0.3 0.3 0.6 BC006717 1.0 1.8 4.8 5.6 BC011479 1.0 1.3 3.9 3.8 BC021353 1.0 0.2 0.2 0.2 BC021353 1.0 0.3 0.2 0.2 BC021353 1.0 0.3 0.3 0.3 BC021407 1.0 1.2 4.4 3.7 BC021429 1.0 0.9 0.3 0.3 BC021522 1.0 2.3 4.0 4.1 BC021842 1.0 1.8 4.5 6.6 BC022135 1.0 0.6 0.3 0.3 BC025169 1.0 0.7 0.2 0.1 BC026867 1.0 0.8 0.3 0.2 BF118393 1.0 0.7 0.3 0.2 BF578669 1.0 0.5 0.3 0.2 BG064632 1.0 10.2 14.7 16.6 BG066982 1.0 0.8 0.3 0.2 BG075321 1.0 0.7 3.7 5.0 BG080055 1.0 0.7 0.3 0.2 BG143461 1.0 0.5 0.3 0.2 BG868949 1.0 1.3 3.6 3.5 BG868949 1.0 1.3 4.4 4.3 BI251603 1.0 1.9 4.0 3.8 BI454991 1.0 2.0 3.7 4.2 BI466783 1.0 0.5 0.2 0.2 BI558298 1.0 1.1 0.3 0.2 BI660196 1.0 1.2 3.6 4.4 BM117243 1.0 1.4 3.3 4.1 BM117243 1.0 1.6 3.6 3.9 BM200151 1.0 1.0 0.3 0.3 BM213835 1.0 0.8 0.3 0.2 BM247465 1.0 0.5 0.2 0.1 C78203 1.0 2.5 3.7 3.4 NM_020562 1.0 1.0 0.3 0.3 NM_026235 1.0 1.3 3.1 7.2 NM_026839 1.0 0.7 0.3 0.2 NM_030697 1.0 0.5 3.4 5.0 NM_054098 1.0 2.1 15.0 24.3 NM_133706 1.0 1.0 0.3 0.2 NM_133775 1.0 1.8 3.2 4.3

Genes encoding non-secretory proteins that demonstrated at least 3-fold differential expression in at least one time-point over a 25 h angiogenesis timecourse. TABLE V Transmembrane proteins differentially regulated during MB114 tubulogenesis Hours of tubulogenesis Name GenBank 1 5 15 25 Description 0610007C21Rik AK002276 1.0 1.5 2.1 3.3 Clone IMAGE: 1513950, mRNA (predicted transmembrane) 1810014L12Rik NM_133706 1.0 1.0 0.3 0.2 RIKEN cDNA 1810014L12 gene (predicted transmembrane) Alcam U95030 1 3.4 4.2 2.6 activated leukocyte cell adhesion molecule Anpep NM_008486 1 3.5 7.0 9.3 alanyl (membrane) aminopeptidase Areg NM_009704 1 0.7 0.2 0.1 amphiregulin calcium channel, voltage- Cacna2d1 NM_009784 1.0 2.3 3.9 4.3 dependent, alpha2/delta subunit 1 Cd14 NM_009841 1.0 2.0 4.0 6.4 CD14 antigen Cd38 BB256012 1.0 4.5 4.8 5.1 CD38 antigen Cd44 X66083 1.0 1.2 0.3 0.2 CD44 antigen Cd53 NM_007651 1.0 2.0 9.6 10.4 CD53 antigen Dtr L07264 1.0 0.4 0.1 0.1 diphtheria toxin receptor Emp2 AF083876 1 2.6 3.1 3.2 epithelial membrane protein 2 Epha2 NM_010139 1.0 0.4 0.2 0.2 Eph receptor A2 Fcgrt NM_010189 1.0 1.1 2.5 6.1 Fc receptor, IgG, alpha chain transporter Islr NM_012043 1.0 1.2 2.4 4.2 immunoglobulin superfamily containing leucine-rich repeat Itga3 NM_013565 1.0 0.9 0.3 0.2 integrin alpha 3 Itga6 BM935811 1.0 1.3 0.1 0.1 integrin alpha 6 Ldlr AF425607 1.0 0.2 0.2 0.2 low density lipoprotein receptor Lrp1 NM_008512 1.0 1.3 3.2 5.5 low density lipoprotein receptor- related protein 1 Lrp2 C80829 1.0 0.5 0.3 0.2 low density lipoprotein receptor- related protein 2 Ly6a BC002070 1.0 0.7 2.3 4.8 lymphocyte antigen 6 complex, locus A Npr3 NM_008728 1 0.5 0.2 0.2 natriuretic peptide receptor 3 P2rx4 AJ251462 1 1.1 3.2 5.2 purinergic receptor P2X, ligand- gated ion channel 4 Pcdh18 AK014140 1.0 0.2 0.3 0.3 protocadherin 18 Pcdhb9 NM_053134 1.0 1.1 3.2 4.7 protocadherin beta 9 Ptpre U35368 1.0 1.0 0.3 0.3 protein tyrosine phosphatase, receptor type, E Ramp1 NM_016894 1.0 1.3 4.0 5.9 receptor (calcitonin) activity modifying protein 1 Sele NM_011345 1.0 1.3 0.3 0.3 selectin, endothelial cell Slc4a3 NM_009208 1 1.7 3.1 4.5 solute carrier family 4 (anion exchanger), member 3 solute carrier family 7 (cationic Slc7a5 BC026131 1 1.4 0.3 0.1 amino acid transporter, y+ system), member 5 Tfrc AK011596 1.0 1.1 0.3 0.3 transferrin receptor Tm4sf12 BB072896 1.0 2.3 3.3 3.5 transmembrane 4 superfamily member 12 Tmc6 BC004840 1.0 2.1 3.4 3.3 transmembrane channel-like gene family 6

Genes encoding transmembrane or membrane-associated proteins that demonstrated at least 3-fold differential expression in at least one time-point over the 25 h angiogenesis timecourse. Identified genes encoding known angiogenic regulators are shown in bold type face. Identified genes encoding putative angiogenic regulators are shown in regular text face. TABLE VI Real-Time PCR analysis of select proteins Hrs. of Tubulogenesis Name 1 5 15 25 ADAMts1 1.0 0.4 1.6 2.4 ADAMts7 1.0 2.0 4.9 5.1 CRELD-2 1.0 11.4 5.8 10.0 CTGF 1.0 0.3 0.4 0.3 Decorin 1.0 3.6 8.4 16.6 ECM1 1.0 4.3 6.3 9.0 Inhibin β-a (Inhβ-a) 1.0 4.9 1.4 1.1 Inhibin β-b (Inhβ-b) 1.0 0.1 0.5 0.7 Integrin α-3 1.0 1.4 0.8 0.3 Integrin α-6 1.0 1.2 0.6 0.4 Lipocalin-7 1.0 0.9 0.6 0.6 Loxl-3 1.0 2.8 18.0 17.9 Lumican 1.0 0.4 0.9 1.7 MAGP-2 1.0 8.4 2.3 4.2 Matrilin-2 1.0 1.6 6.7 8.0 Nephronectin 1.0 0.9 0.5 0.5 SerpinE2 1.0 0.8 5.1 10.1 SMOC-2 1.0 21.5 58.3 13.1 TIMP-3 1.0 2.5 0.5 0.5 Real-time PCR analysis was conducted to confirm differential expression of selected genes from microarray analysis.

Example 2

The following example describes the effects of putative angiogenic gene expression on EC activities-coupled to angiogenesis.

The microarray analyses described in Example 1 identified numerous genes whose expression is regulated by angiogenesis, indicating that the expression of these genes is required during vessel formation. To test this hypothesis and to identify novel regulators of EC activities-coupled to angiogenesis, a series of in vitro assays was performed that modeled angiogenesis activation in ECs (Albig et al, 2006; Albig and Schiemann, 2004; Albig and Schiemann, 2005). In doing so, bicistronic retroviral transduction of MB114 cells was used to stably express six identified secretory proteins, namely matrilin-2, CRELD-2 (cysteine-rich with EGF-Like domains-2), MAGP-2, lumican, SMOC-2 (secreted modular calcium-binding protein-2), and ECM-1, (extracellular protein-1), and one putative transmembrane protein, AK002276. Immunoblotting and semi-quantitative real-time PCR analyses both showed that the expression of all individual transgenes were readily detected in MB114 cells (FIGS. 7A and 7B). In these experiments, MB114 cells were infected with retrovirus encoding either GFP (i.e., control) or various potential angiogenic agents as indicated. Afterward, infected cells were FACS-sorted by GFP expression (highest 10%) to establish stable polyclonal populations of transgenic MB114 cells. Transgene expression was detected by immunoblotting nickel-captured secretory proteins with anti-Myc antibodies, except AK002276 which was captured from detergent-solubilized cell extracts (FIG. 7A) and by performing semi-quantitative real-time PCR (FIG. 7B).

FIG. 1A show results from an experiment in which serum-starved MB114 cells, stably expressing either GFP or various putative angiogenic agents, were stimulated in the absence or presence of either bFGF (50 ng/ml) or EGF (10 ng/ml) for 24 h at 37° C. Differences in MB114 cell DNA synthesis was determined by measuring [³H]thymidine incorporation into cellular DNA. Functionally, MAGP-2 and SMOC-2 expression significantly enhanced the proliferative response of MB114 cells to bFGF, while MAGP-2 and AK002276 expression significantly enhanced that to EGF (FIG. 1A). In contrast, expression of all other transgenes failed to effect the proliferative response of MB114 cells to either bFGF or EGF (data not shown). FIG. 1B shows that SMOC-2, MAGP-2, and CRELD-2 expression all significantly induced MB114 cell invasion through synthetic basement membranes, a response that was not mimicked by expression of additional transgenes (data not shown). In this experiment, invasion of MB114 cells expressing either GFP or various putative angiogenic agents through synthetic basement membranes was determined over 48 h using a modified Boyden-chamber assay.

The inventors' previous studies have associated stimulation of p38 MAPK activity with angiogenesis of MB114 cells and, conversely, inhibition of p38 MAPK activity with angiostasis of MB114 cells (Albig et al, 2006; Albig and Schiemann, 2004; Albig and Schiemann, 2005). Serum-starved MB114 cells expressing MAGP-2 (FIG. 1C) or lumican (FIG. 1D) were stimulated with either bFGF (50 ng/ml) or EGF (10 ng/ml) 0-15 min as indicated in the figures. The phosphorylation status of p38 MAPK was determined by immunoblotting whole cell lysates with phospho-specific p38 MAPK antibodies (p38-P). Differences in protein loading were monitored by reprobing stripped membranes with anti-p38 MAPK polyclonal antibodies (p38). FIG. 1C shows that MAGP-2 expression significantly enhanced p38 MAPK phosphorylation in MB114 cells stimulated with either bFGF or EGF stimulation. In contrast, lumican expression significantly inhibited p38 MAPK activation in MB114 cells treated with either growth factor (FIG. 1D).

Finally, it was determined whether expression of these putative angiogenic factors could effect the angiogenic sprouting of quiescent MB114 cells monolayers. MB114 cells expressing either GFP or various putative angiogenic agents were grown to confluency, and subsequently were overlaid with rat tail collagen matrices. Angiogenic sprouting by quiescent EC monolayers was stimulated by inclusion of 10% FBS and allowed to proceed for 5 days. The quantity of invading angiogenic sprouts was determined by manual counting under a light microscope. FIG. 1E shows that expression of CRELD-2, matrillin-2, or AK002276 failed to significantly affect MB114 cell angiogenic sprouting in response to serum. In stark contrast, expression of MAGP-2 or SMOC-2 both significantly increased the sprouting of MB114 cells cell sprouting, while that of lumican and ECM-1 significantly decreased the ability of MB114 cells to form angiogenic sprouts in collagen matrices (FIG. 1E).

Collectively, these findings demonstrate that tubulating ECs upregulate expression of lumican and ECM-1 during the latter stages of angiogenesis, consistent with their involvement in mediating angiogenesis resolution. Accordingly, both proteins antagonized angiogenic sprouting in MB114 cells, and as such, the inventors propose lumican and ECM-1 as novel mediators of angiostasis. Conversely, tubulating ECs were observed to upregulate expression of MAGP-2 and SMOC-2 during the early stages of angiogenesis, implicating their involvement in mediating angiogenesis activation. Indeed, both proteins stimulated various angiogenic activities, including angiogenic sprouting in MB114 cells. Thus, it is proposed herein that MAGP-2 and SMOC-2 are novel mediators of angiogenesis. Because MAGP-2 was the only protein to exhibit angiogenic activity in all measured indices in vitro, the inventors chose to further characterize the molecular mechanisms whereby MAGP-2 induces angiogenesis in quiescent ECs.

Example 3

The following example demonstrates that MAGP-2 promotes angiogenesis in vivo.

The ability of MAGP-2 to stimulate EC activities coupled to angiogenesis in vitro indicated that MAGP-2 may function to induce vessel formation in vivo. The inventors tested this hypothesis by utilizing the Matrigel plug implantation assay, which monitors the ability of various angiogenic agents to alter vessel formation and infiltration into Matrigel plugs implanted subcutaneously into normal mice. In doing so, first, recombinant FLAG-tagged MAGP-2 (rMAGP-2) was expressed and purified from bacterial cells (FIG. 2A). More particularly, recombinant FLAG-tagged MAGP-2 (rMAGP-2) was purified from detergent-solubilized bacterial cell extracts by anti-FLAG chromatography. MAGP-2 purity was monitored by coomassie staining, and by immunoblotting with anti-FLAG M2 monoclonal antibodies (FIG. 2A; right panel). rMAGP-2 (1 μg/ml) stimulated angiogenic sprouting of quiescent MB114 cell monolayers (FIG. 2A; left panel). Similar to its constitutive expression in MB114 cells, purified rMAGP-2 protein (1 μg/ml) also was found to stimulate angiogenic sprouting of quiescent MB114 cells, thereby demonstrating that these rMAGP-2 preparations were biologically active (FIG. 2A). To further demonstrate that MAGP-2 promotes angiogenesis in vivo, C57BL/6 female mice were injected subcutaneously with Matrigel supplemented either with diluent (D), bFGF (50 ng/ml, LD; or 300 ng/ml, HD), or bFGF (50 ng/ml) in combination with MAGP-2 (1 μg/ml). Mice were sacrificed on day 10 and the plugs harvested and photographed (FIG. 2B; left panels). Afterward, the Matrigel plugs were fixed, sectioned, and stained with Masson's trichrome to visualize infiltrating blood vessels (FIG. 2B; right panels; arrows denote blood vessels), which were quantified by manual counting under a light microscope. FIG. 2B shows that bFGF dose-dependently stimulated significant vascularization of implanted Matrigel plugs. Importantly, rMAGP-2 administration (1 μg/ml) significantly increased the development and infiltration of vessels into Matrigel plugs supplemented with bFGF as compared to those solely containing bFGF (FIG. 2B). Collectively, these findings, together with the in vitro analyses, provide strong evidence implicating MAGP-2 as a bona fide promoter of angiogenesis.

Example 4

The following example demonstrates that MAGP-2 inhibits Notch1 signaling.

MAGP-2 can interact physically with Notch1 and its ligand, Jagged-1 (Miyamoto et al, 2006; Nehring et al, 2005), resulting in the ectodomain shedding of both molecules from the cell surface. Notch signaling also plays an essential role in regulating normal vessel development and angiogenesis in mammals (Leong and Karsan, 2005; Shawber and Kitajewski, 2004). Given these two facts, the inventors hypothesized that MAGP-2 promotes angiogenesis by modulating Notch1 signaling. To test this hypothesis, first measured were changes in luciferase expression driven by a Hes1-luciferase reporter gene whose expression is induced by NotchI activation (Iso et al, 2003). MB114 and HUVEC cells were transiently transfected either with pHesI-luciferase, pCMV-β-gal, and MAGP-2 cDNAs, or with pHes1-luciferase and pCMV-β-gal cDNAs and subsequently stimulated with rMAGP-2 (1 or 5 μg/ml). Afterward, luciferase and β-gal activities contained in detergent-solubilized cell extracts were measured. In addition, GFP- and MAGP-2-expressing MB114 cells were transiently transfected with pHes1-luciferase and pCMV-β-gal cDNAs, together with or without Jagged-1 cDNA as indicated. Afterward, luciferase and β-gal activities were measured as above. FIG. 3A shows that MAGP-2 expression in or rMAGP-2 treatment of either MB114 or HUVEC cells repressed Hes1-driven luciferase activity. More importantly, MAGP-2 expression abrogated the ability of Jagged-1 to induce Hes1-luciferase activity in MB114 cells (FIG. 3B), suggesting that MAGP-2 functions to antagonize Jagged-1 and, consequently, Notch1 signaling in ECs.

Activation of Notch1 signaling involves three proteolytic processing events, termed S1, S2, and S3, that produce three distinct Notch1 fragments, termed TMIC, NEXT, and NICD, respectively (Mumm et al, 2000). NICD production is mediated by a gamma-secretase cleavage reaction that cuts Notch1 at a membrane proximal cytoplasmic site (Mumm et al, 2000), resulting in the release and subsequent translocation of NICD to the nucleus where it regulates the expression of Notch1-responsive genes, including Hes1 (Iso et al, 2003). The findings described above indicate that MAGP-2 antagonizes Notch1 signaling, and as such, indicate that MAGP-2 may do so by inhibiting Notch1 proteolytic processing. The inventors tested this possibility by transiently transfecting human 293T cells with cDNAs encoding Myc-tagged versions of Notch1, Jagged-1, and MAGP-2 in all combinations, and subsequently monitored changes in NICD production and accumulation by immunoblot analyses using anti-Myc monoclonal antibodies. As expected, Jagged-1 expression significantly enhanced Notch1 processing and the production of NICD as compared to cells solely expressing Notch1 (FIG. 4A). Importantly, the ability of Jagged-1 to induce Notch1 cleavage and NICD production in 293T cells was reduced significantly by co-expression of MAGP-2 (FIG. 4A). Thus, these findings indicate that MAGP-2 inhibits Notch1 signaling and Hes1 expression in part by preventing Notch1 processing and NICD production.

To further investigate the impact of MAGP-2 on Notch1 processing and NICD accumulation, the inventors took advantage of recent findings showing that the ability of TGF-β to induce Hes1 promoter activity requires Smad3 to interact physically with NICD (Blokzijl et al, 2003), a reaction that is dispensable for canonical Smad3-mediated signaling stimulated by TGF-β (Blokzijl et al, 2003). It was therefore reasoned that the ability of MAGP-2 to inhibit NICD production in ECs would reduce the capacity of TGF-β to induce luciferase expression driven by the Hes1 promoter, but not that driven by the synthetic Smad2/3-binding element (SBE). GFP- and MAGP-2-expressing MB114 cells were transiently transfected with either pHesI- or pSBE-luciferase, both together with pCMV-β-gal as indicated in FIG. 4B. Afterward, the resulting transfectants were stimulated overnight with increasing concentrations of TGF-β1 (0-5 ng/ml). MAGP-2 expression in MB114 cells significantly decreased the ability of TGF-β to stimulate Hes1-luciferase activity, but had no effect on its stimulation of SBE-luciferase activity (FIG. 4B). Similar effects of MAGP-2 on TGF-β-stimulated Hes1- and SBE-luciferase activities also were observed in HUVEC cells, indicating that MAGP-2-mediated inhibition of Notch1 processing and NICD production was not restricted solely to MB114 cells (data not shown). Collectively, these findings demonstrate that MAGP-2 antagonizes Notch1 signaling by preventing its cleavage and ultimate release of the Notch1 signaling fragment, NICD.

Example 5

The following examples shows that MAGP-2 promotes angiogenesis by antagonizing Notch signaling.

Based on the findings described in the Examples above, the inventors hypothesized that MAGP-2 promotes angiogenesis by antagonizing Notch1 signaling. To test this hypothesis, it was first determined whether inhibiting Notch signaling in MB114 cells would enhance their angiogenic sprouting. In doing so, MB114 cells were transiently transfected with the Hes1-luciferase reporter gene (and pCMV-β-gal cDNA as control), and subsequently were treated overnight with or without the highly specific gamma-secretase inhibitor, DAPT (Sastre et al, 2001), which inhibits S3-mediated cleavage of Notch1 and, consequently, NICD-mediated induction of Hes1 expression. Afterward, luciferase and β-gal activities were determined. As expected, DAPT administration (10 μM) significantly inhibited Hes1 promoter activity in MB114 cells (FIG. 5A). More importantly, MB114 cells treated with DAPT formed significantly more angiogenic sprouts than did their untreated counterparts (FIG. 5B). In this experiment, quiescent MB114 cell monolayers were overlaid with rat tail collagen matrices, and were induced to form angiogenic sprouts by addition of 10% FBS supplemented with or without DAPT (10 μM). Five days later the number of invading angiogenic spouts were quantified by manual counting on a light microscope. Based on these findings, the inventors conclude that Notch activation functions in mediating angiostasis in MB114 cells. This conclusion is bolstered further by the inventors' observation that the Notch ligands Jagged-1 and Delta-like-4, and the Hes1 transcription factor were all strongly downregulated in tubulating MB114 cells (Table VII). Collectively, these findings indicate that Notch1 signaling antagonizes angiogenic sprouting in MB114 cells, and that downregulation of Notch1 signaling components is necessary for angiogenesis activation in MB114 cells. TABLE VII Expression of Notch signaling components During Tubulogenesis Hours of Tubulogenesis Name Genbank 1 5 15 25 DII1 NM_007865 1.0 0.9 1.3 1.1 DII3 AB013440 1.0 0.8 0.6 0.9 DII4 AK004739 1.0 1.2 0.3 0.4 Jag1 AA880220 1.0 0.7 0.2 0.2 Jag2 AV264681 1.0 0.4 0.7 1.3 Notch1 NM_008714 1.0 1.4 0.6 0.7 Notch2 D32210 1.0 1.1 1.1 1.2 Notch3 NM_008716 1.0 0.9 1.3 1.5 Notch4 NM_010929 1.0 1.1 1.1 1.1 Hes1 BC018375 1.0 0.5 0.2 0.1 Expression of various components of the Notch signaling pathway during MB114 cell tubulogenesis on Matrigel matrices.

Having shown that Notch1 signaling mediates angiostasis in MB114 cells, the inventors next asked whether MAGP-2 promotes angiogenesis in MB114 cells via its ability to antagonize Notch signaling. To do so, MAGP-2-expressing MB114 cells were engineered to constitutively express active Notch1 NICD fragment in an attempt to overcome the block of Notch processing mediated by MAGP-2. More particularly, GFP-, MAGP-2-, and MAGP-2/N1ICD-expressing MB114 cells were transiently transfected with pHes1-luciferase and pCMV-β-gal cDNAs. Luciferase and P-gal activities were determined 48 h post-transfection. As the inventors observed previously, MAGP-2 expression reduced Hes1-luciferase activity in MB114 cells (FIG. 5C), a reaction that was bypassed by co-expression of NICD in these cells (FIG. 5C). More importantly, the ability of MAGP-2 to promote angiogenic sprouting was prevented completely by constitutive N1ICD expression in MB114 cells (FIG. 5D). In this experiment, quiescent monolayers of GFP-, MAGP-2-, and MAGP-2/N1ICD-expressing MB114 cells were overlaid with rat tail collagen matrices and incubated in the absence or presence of 10% FBS for 5 days. Afterward, the number of invading angiogenic sprouts were determined by manual counting under a light microscope. Taken together, these results demonstrate that Notch1 activation antagonizes angiogenesis in MB114 cells, and most notably, that MAGP-2 promotes angiogenesis in part via its ability to antagonize Notch1 processing and signaling in ECs.

Example 6

The following example shows that MAGP-2 is expressed aberrantly in the majority of human uterine tumors.

Radiolabeled cDNA probes corresponding to either murine MAGP-2 (FIG. 8A; upper panel) or human ubiquitin (FIG. 8A; lower panel) were hybridized to matched human normal:tumor cDNA array. The resulting phosphor-images depict MAGP-2 and ubiquitin expression in paired normal (upper spot) and malignant (bottom spot) uterine tissue. MAGP-2 expression was normalized to that of ubiquitin, followed by a determination of tumor:normal tissue MAGP-2 expression ratios. Ratios ≧2 or ≦0.5 were considered significant. The results showed that MAGP-2 is expressed aberrantly in the majority of human uterine tumors tested.

Each publication or other reference disclosed below and elsewhere herein is incorporated herein by reference in its entirety.

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While various embodiments of the present invention have been described in detail, it is apparent that modifications and adaptations of those embodiments will occur to those skilled in the art. It is to be expressly understood, however, that such modifications and adaptations are within the scope of the present invention, as set forth in the following claims. 

1. A method to regulate angiogenesis in cells or a tissue of a patient, comprising regulating the expression or biological activity in the cells or tissue of any one or more biomarkers selected from the group consisting of a biomarker represented in any one or more of Table I, Table IV, Table V, and Table VI.
 2. The method of claim 1, wherein the biomarkers are any one or more of the biomarkers in Table VI.
 3. The method of claim 1, wherein the biomarkers are any one or more of the biomarkers selected from the group consisting of: ADAMts7, CRELD-2, Decorin, ECM1, Inhibin β-b, Integrin α-3, Integrin α-6, Lipocalin-7, Loxl-3, Lumican, MAGP-2, Matrilin-2, Nephronectin, SerpinE2, and SMOC-2.
 4. The method of claim 1, wherein the biomarkers are any one or more of the biomarkers selected from the group consisting of: 0610007C21Rik, apoptbsis related protein APR-3, 1810014L12Rik, Cd14 (encoding CD14 antigen represented herein by SEQ ID NO:5 and SEQ ID NO:6), Cd38 (comprising a nucleic acid sequence represented herein by SEQ ID NO:7 and encoding CD38 antigen); Cd53 (encoding CD53 antigen represented herein by SEQ ID NO:8 and SEQ ID NO:9), Emp2 (encoding epithelial membrane protein represented herein by SEQ ID NO:10 and SEQ ID NO:11), Fcgrt (encoding Fc receptor (IgG, alpha chain transporter) represented herein by SEQ ID NO:12 and SEQ ID NO:13), Islr (encoding immunoglobulin superfamily containing leucine-rich repeat represented herein by SEQ ID NO:14 and SEQ ID NO:15); Lrp2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:16 and SEQ ID NO:17 and encoding low density lipoprotein receptor-related protein 2); Ly6a (encoding lymphocyte antigen 6 complex, locus A represented herein by SEQ ID NO:18); P2rx4 (encoding purinergic receptor P2X, ligand-gated ion channel 4, represented herein by SEQ ID NO:19 and SEQ ID NO:20; Pcdhb9 (encoding protocadherin beta 9 represented herein by SEQ ID NO:21 and SEQ ID NO:22); Ptpre (encoding protein tyrosine phosphatase receptor type E represented herein by SEQ ID NO:23 and SEQ ID NO:24); Slc4a3 (encoding solute carrier family 4 (anion exchanger) member 3, represented herein by SEQ ID NO:25 and SEQ ID NO:26); and/or Tmc6 (encoding transmembrane channel-like gene family 6, represented herein by SEQ ID NO:27).
 5. The method of claim 1, wherein the biomarkers are any one or more of the biomarkers selected from the group consisting of: 9130213B05Rik (encoding a protein represented herein by SEQ ID NO:29); C1s (encoding complement component 1, s subcomponent, represented herein by SEQ ID NO:34 and SEQ ID NO:35); C3 (encoding complement component 3 represented herein by SEQ ID NO:30 and SEQ ID NO:31); Cfh (comprising a nucleic acid sequence represented herein by SEQ ID NO:32 and SEQ ID NO:33 and encoding complement component factor h); Col9a3 (comprising a nucleic acid sequence represented herein by SEQ ID NO:36 and SEQ ID NO:37 and encoding procollagen, type IX, alpha 3); Grem1 (encoding cysteine knot superfamily 1, BMP antagonist 1, represented herein by SEQ ID NO:38 and SEQ ID NO:39); Loxl3 (encoding lysyl oxidase-like 3, represented herein by SEQ ID NO:40 and SEQ ID NO:41); MAGP-2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:124 and SEQ ID NO:125 and encoding microfibrillar associated protein 5, represented herein by SEQ ID NO:42 and SEQ ID NO:43); Mglap (encoding matrix gamma-carboxyglutamate (gla) protein represented herein by SEQ ID NO:44 and SEQ ID NO:45); Naga (encoding N-acetyl galactosaminidase, alpha, represented herein by SEQ ID NO:46 and SEQ ID NO:47); Nbl1 (encoding neuroblastoma, suppression of tumorigenicity 1, represented herein by SEQ ID NO:48 and SEQ ID NO:49); Ngfb (encoding nerve growth factor, beta, represented herein by SEQ ID NO:50 and SEQ ID NO:51), Npnt (represented herein by SEQ ID NO:52 and SEQ ID NO:53 and encoding nephronectin); Olfm1 (encoding olfactomedin 1, represented herein by SEQ ID NO:54 and SEQ ID NO:55); and/or U90926 (encoding a protein represented herein by SEQ ID NO:56).
 6. The method of claim 1, wherein the biomarker is MAGP-2.
 7. The method of claim 1, wherein the step of regulating comprises contacting the cells or tissue of from the patient with an antagonist of the biomarker.
 8. The method of claim 1, wherein the step of regulating comprises contacting the cells or tissue of from the patient with the biomarker or a biologically active homologue or agonist thereof.
 9. The method of claim 1, wherein the step of regulating comprises expressing a recombinant nucleic acid molecule encoding the biomarker or a homologue thereof in the tissue of the patient.
 10. The method of claim 1, wherein angiogenesis is upregulated.
 11. The method of claim 10, wherein the patient has experienced ischemia or stroke.
 12. The method of claim 1, wherein angiogenesis is downregulated.
 13. The method of claim 12, wherein the patient has cancer.
 14. A method to reduce tumorigenicity in a patient, comprising regulating the expression or biological activity of any one or more biomarkers selected from the group consisting of a biomarker represented in any one or more of Table I, Table IV, Table V, and Table VI.
 15. The method of claim 14, wherein the biomarkers are any one or more of the biomarkers in Table VI.
 16. The method of claim 14, wherein the biomarkers are any one or more of the biomarkers selected from the group consisting of: ADAMts7, CRELD-2, Decorin, ECM1, Inhibin β-b, Integrin α-3, Integrin α-6, Lipocalin-7, Loxl-3, Lumican, MAGP-2, Matrilin-2, Nephronectin, SerpinE2, and SMOC-2.
 17. The method of claim 14, wherein the biomarkers are any one or more of the biomarkers selected from the group consisting of: 0610007C21Rik, apoptosis related protein APR-3, 1810014L12Rik, Cd14 (encoding CD14 antigen represented herein by SEQ ID NO:5 and SEQ ID NO:6), Cd38 (comprising a nucleic acid sequence represented herein by SEQ ID NO:7 and encoding CD38 antigen); Cd53 (encoding CD53 antigen represented herein by SEQ ID NO:8 and SEQ ID NO:9), Emp2 (encoding epithelial membrane protein represented herein by SEQ ID NO:10 and SEQ ID NO:11), Fcgrt (encoding Fc receptor (IgG, alpha chain transporter) represented herein by SEQ ID NO:12 and SEQ ID NO:13), Islr (encoding immunoglobulin superfamily containing leucine-rich repeat represented herein by SEQ ID NO:14 and SEQ ID NO:15); Lrp2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:16 and SEQ ID NO:17 and encoding low density lipoprotein receptor-related protein 2); Ly6a (encoding lymphocyte antigen 6 complex, locus A represented herein by SEQ ID NO:18); P2rx4 (encoding purinergic receptor P2X, ligand-gated ion channel 4, represented herein by SEQ ID NO:19 and SEQ ID NO:20; Pcdhb9 (encoding protocadherin beta 9 represented herein by SEQ ID NO:21 and SEQ ID NO:22); Ptpre (encoding protein tyrosine phosphatase receptor type E represented herein by SEQ ID NO:23 and SEQ ID NO:24); Slc4a3 (encoding solute carrier family 4 (anion exchanger) member 3, represented herein by SEQ ID NO:25 and SEQ ID NO:26); and/or Tmc6 (encoding transmembrane channel-like gene family 6, represented herein by SEQ ID NO:27).
 18. The method of claim 14, wherein the biomarkers are any one or more of the biomarkers selected from the group consisting of: 9130213B05Rik (encoding a protein represented herein by SEQ ID NO:29); C1s (encoding complement component 1, s subcomponent, represented herein by SEQ ID NO:34 and SEQ ID NO:35); C3 (encoding complement component 3 represented herein by SEQ ID NO:30 and SEQ ID NO:31); Cfh (comprising a nucleic acid sequence represented herein by SEQ ID NO:32 and SEQ ID NO:33 and encoding complement component factor h); Col9a3 (comprising a nucleic acid sequence represented herein by SEQ ID NO:36 and SEQ ID NO:37 and encoding procollagen, type IX, alpha 3); Grem1 (encoding cysteine knot superfamily 1, BMP antagonist 1, represented herein by SEQ ID NO:38 and SEQ ID NO:39); Loxl3 (encoding lysyl oxidase-like 3, represented herein by SEQ ID NO:40 and SEQ ID NO:41); MAGP-2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:124 and SEQ ID NO:125 and encoding microfibrillar associated protein 5, represented herein by SEQ ID NO:42 and SEQ ID NO:43); Mglap (encoding matrix gamma-carboxyglutamate (gla) protein represented herein by SEQ ID NO:44 and SEQ ID NO:45); Naga (encoding N-acetyl galactosaminidase, alpha, represented herein by SEQ ID NO:46 and SEQ ID NO:47); Nbl1 (encoding neuroblastoma, suppression of tumorigenicity 1, represented herein by SEQ ID NO:48 and SEQ ID NO:49); Ngfb (encoding nerve growth factor, beta, represented herein by SEQ ID NO:50 and SEQ ID NO:51), Npnt (represented herein by SEQ ID NO:52 and SEQ ID NO:53 and encoding nephronectin); Olfm1 (encoding olfactomedin 1, represented herein by SEQ ID NO:54 and SEQ ID NO:55); and/or U90926 (encoding a protein represented herein by SEQ ID NO:56).
 19. The method of claim 14, wherein the biomarker is MAGP-2.
 20. A method to identify a compound that regulates angiogenesis, comprising: a) detecting an initial level of the expression or activity of one or more biomarkers in a cell or soluble product derived therefrom, wherein the biomarker is a biomarker selected from the group consisting of a biomarker represented in any one or more of Table I, Table IV, Table V, and Table VI; b) contacting the cell with a test compound; c) detecting a level of the biomarker expression or activity in the cell or soluble product derived therefrom after contact of the cell with the compound; and, d) selecting a compound that changes the level of biomarker expression or activity in the cell or soluble product therefrom, as compared to in the absence of the compound and/or as compared to the initial level of biomarker expression or activity, as a compound that regulates angiogenesis.
 21. The method of claim 20, wherein the biomarker is a biomarker in Table VI.
 22. The method of claim 20, wherein the biomarker is a biomarker selected from the group consisting of: ADAMts7, CRELD-2, Decorin, ECM1, Inhibin β-b, Integrin α-3, Integrin α-6, Lipocalin-7, Loxl-3, Lurnican, MAGP-2, Matrilin-2, Nephronectin, SerpinE2, and SMOC-2.
 23. The method of claim 20, wherein the biomarker is a biomarker selected from the group consisting of: 0610007C21Rik, apoptosis related protein APR-3, 1810014L12Rik, Cd14 (encoding CD14 antigen represented herein by SEQ ID NO:5 and SEQ ID NO:6), Cd38 (comprising a nucleic acid sequence represented herein by SEQ ID NO:7 and encoding CD38 antigen); Cd53 (encoding CD53 antigen represented herein by SEQ ID NO:8 and SEQ ID NO:9), Emp2 (encoding epithelial membrane protein represented herein by SEQ ID NO:10 and SEQ ID NO:11), Fcgrt (encoding Fc receptor (IgG, alpha chain transporter) represented herein by SEQ ID NO:12 and SEQ ID NO:13), Islr (encoding immunoglobulin superfamily containing leucine-rich repeat represented herein by SEQ ID NO:14 and SEQ ID NO:15); Lrp2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:16 and SEQ ID NO:17 and encoding low density lipoprotein receptor-related protein 2); Ly6a (encoding lymphocyte antigen 6 complex, locus A represented herein by SEQ ID NO:18); P2rx4 (encoding purinergic receptor P2X, ligand-gated ion channel 4, represented herein by SEQ ID NO:19 and SEQ ID NO:20; Pcdhb9 (encoding protocadherin beta 9 represented herein by SEQ ID NO:21 and SEQ ID NO:22); Ptpre (encoding protein tyrosine phosphatase receptor type E represented herein by SEQ ID NO:23 and SEQ ID NO:24); Slc4a3 (encoding solute carrier family 4 (anion exchanger) member 3, represented herein by SEQ ID NO:25 and SEQ ID NO:26); and/or Tmc6 (encoding transmembrane channel-like gene family 6, represented herein by SEQ ID NO:27).
 24. The method of claim 20, wherein the biomarker is a biomarker selected from the group consisting of: 9130213B05Rik (encoding a protein represented herein by SEQ ID NO:29); C1s (encoding complement component 1, s subcomponent, represented herein by SEQ ID NO:34 and SEQ ID NO:35); C3 (encoding complement component 3 represented herein by SEQ ID NO:30 and SEQ ID NO:31); Cfh (comprising a nucleic acid sequence represented herein by SEQ ID NO:32 and SEQ ID NO:33 and encoding complement component factor h); Col9a3 (comprising a nucleic acid sequence represented herein by SEQ ID NO:36 and SEQ ID NO:37 and encoding procollagen, type IX, alpha 3); Grem1 (encoding cysteine knot superfamily 1, BMP antagonist 1, represented herein by SEQ ID NO:38 and SEQ ID NO:39); Loxl3 (encoding lysyl oxidase-like 3, represented herein by SEQ ID NO:40 and SEQ ID NO:41); MAGP-2 (comprising a nucleic acid sequence represented herein by SEQ ID NO:124 and SEQ ID NO:125 and encoding microfibrillar associated protein 5, represented herein by SEQ ID NO:42 and SEQ ID NO:43); Mglap (encoding matrix gamma-carboxyglutamate (gla) protein represented herein by SEQ ID NO:44 and SEQ ID NO:45); Naga (encoding N-acetyl galactosaminidase, alpha, represented herein by SEQ ID NO:46 and SEQ ID NO:47); Nbl1 (encoding neuroblastoma, suppression of tumorigenicity 1, represented herein by SEQ ID NO:48 and SEQ ID NO:49); Ngfb (encoding nerve growth factor, beta, represented herein by SEQ ID NO:50 and SEQ ID NO:51), Npnt (represented herein by SEQ ID NO:52 and SEQ ID NO:53 and encoding nephronectin); Olfm1 (encoding olfactomedin 1, represented herein by SEQ ID NO:54 and SEQ ID NO:55); and/or U90926 (encoding a protein represented herein by SEQ ID NO:56).
 25. The method of claim 20, wherein the biomarker is MAGP-2.
 26. A method to identify a compound useful for inhibition of tumor growth or malignancy, comprising: a) detecting an initial level of the expression or activity of one or more biomarkers in a cell or soluble product derived therefrom, wherein the biomarker is a biomarker represented in any one or more of Table I, Table IV, Table V, and Table VI; b) contacting the tumor cell with a test compound; c) detecting a level of biomarker expression or activity in the tumor cell or soluble product derived therefrom after contact of the tumor cell with the compound; and, d) selecting a compound that changes the level of the biomarker expression or activity in the tumor cell or soluble product therefrom, as compared to the initial level of biomarker expression or activity, toward a baseline level of biomarker expression or activity established from a non-tumor cell, wherein the selected compound is predicted to be useful for inhibition of tumor growth or malignancy.
 27. A method for assessing the presence of tumor cells or potential therefore in a patient, comprising: a) detecting a level of expression or activity of the expression or activity of one or more biomarkers in a test sample from a patient to be diagnosed, wherein the biomarker is a biomarker represented in any one or more of Table I, Table IV, Table V, and Table VI; and b) comparing the level of expression or activity of the biomarker in the test sample to a baseline level of biomarker expression or activity established from a control sample; wherein detection of a statistically significant difference in the biomarker expression or activity in the test sample, as compared to the baseline level of biomarker expression or biological activity, is an indicator of the presence of tumor cells or the potential therefore in the test sample as compared to cells in the control sample.
 28. The method of claim 27, wherein the step of detecting comprises detecting biomarker mRNA transcription by cells in the test sample.
 29. The method of claim 27, wherein the step of detecting is by a method selected from the group consisting of polymerase chain reaction (PCR), reverse transcriptase-PCR (RT-PCR), in situ hybridization, Northern blot, sequence analysis, gene microarray analysis, and detection of a reporter gene.
 30. The method of claim 27, wherein the step of detecting comprises detecting biomarker protein in the test sample.
 31. The method of claim 27, wherein the step of detecting is by a method selected from the group consisting of immunoblot, enzyme-linked immunosorbant assay (ELISA), radioimmunoassay (RIA), immunoprecipitation, immunohistochemistry and immunofluorescence.
 32. The method of claim 27, wherein the step of detecting comprises detecting biomarker biological activity in the test sample.
 33. The method of claim 27, wherein the step of detecting comprises measuring proliferation of cells expressing the biomarker, measuring angiogenic sprouting of cells expressing the biomarker, and measuring migration and invasion ability of endothelial cells expressing the biomarker.
 34. The method of claim 27, wherein the test sample is from a source selected from the group consisting of: breast, kidney, ovary, colon, and uterus, in the patient.
 35. The method of claim 27, wherein the test sample is from a patient being diagnosed for cancer and wherein the baseline level is established from a negative control sample that is established as non-tumorigenic.
 36. The method of claim 27, wherein the baseline level is established by a method selected from the group consisting of: (1) establishing a baseline level of biomarker expression or activity in an autologous control sample from the patient, wherein the autologous sample is from a same cell type, tissue type or bodily fluid type as the test sample of step (a); (2) establishing a baseline level of biomarker expression or activity from at least one previous detection of biomarker expression or activity in a previous test sample from the patient, wherein the previous test sample was of a same cell type, tissue type or bodily fluid type as the test sample of step (a); and, (3) establishing a baseline level of biomarker expression or activity from an average of control samples of a same cell type, tissue type or bodily fluid type as the test sample of step (a), the control samples having been obtained from a population of matched individuals.
 37. An assay kit for assessing angiogenesis or the presence of tumor cells in a patient, comprising: a) a reagent for detecting the expression or activity of a biomarker in a test sample, wherein the biomarker is a biomarker represented in any one or more of Table I, Table IV, Table V, and Table VI; and b) a reagent for detecting a control marker characteristic of a cell or tissue type that is in the test sample or that is secreted into the test sample by the cell or tissue.
 38. The assay kit of claim 36, wherein the reagent of (a) is selected from the group consisting of: a hybridization probe of at least about 8 nucleotides that hybridizes under stringent hybridization conditions to a nucleic acid molecule encoding the biomarker or a fragment thereof, an oligonucleotide primer for amplification of mRNA encoding the biomarker or a fragment thereof; and an antibody that selectively binds to the biomarker.
 39. The assay kit of claim 36, wherein the reagent of (b) is selected from the group consisting of: a hybridization probe of at least about 8 nucleotides that hybridizes under stringent hybridization conditions to a nucleic acid molecule encoding the control marker or a fragment thereof; an oligonucleotide primer for amplification of mRNA encoding the control marker or a fragment thereof; and an antibody that selectively binds to the control marker.
 40. The assay kit of claim 36, wherein the reagents of (a) and (b) are suitable for use in a method of detection selected from the group consisting of immunohistochemistry and immunofluorescence.
 41. A method to reduce angiogenesis in cells or a tissue of a patient, comprising decreasing the expression or biological activity of Microfibril-associated glycoprotein-2 (MAGP-2) in the cells or tissue.
 42. A method to promote angiogenesis in cells or a tissue of a patient, comprising increasing the expression or biological activity of MAGP-2 in the cells or tissue.
 43. Use of MAGP-2 or a fragment or homologue thereof, or a nucleic acid molecule encoding MAGP-2 or a fragment or homologue thereof, or an agonist or antagonist of MAGP-2, in the preparation of a medicament for the regulation of angiogenesis. 